201
|
Santin I, Eizirik DL. Candidate genes for type 1 diabetes modulate pancreatic islet inflammation and β-cell apoptosis. Diabetes Obes Metab 2013; 15 Suppl 3:71-81. [PMID: 24003923 DOI: 10.1111/dom.12162] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/17/2013] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have identified more than 50 loci associated with genetic risk of type 1 diabetes (T1D). Several T1D candidate genes have been suggested or identified within these regions, but the molecular mechanisms by which they contribute to insulitis and β-cell destruction remain to be clarified. More than 60% of the T1D candidate genes are expressed in human pancreatic islets, suggesting that they contribute to T1D by regulating at least in part pathogenic mechanisms at the β-cell level. Recent studies by our group indicate that important genetically regulated pathways in β-cells include innate immunity and antiviral activity, involving RIG-like receptors (particularly MDA5) and regulators of type I IFNs (i.e. PTPN2 and USP18), and genes related to β-cell phenotype and susceptibility to pro-apoptotic stimuli (i.e. GLIS3). These observations reinforce the concept that the early pathogenesis of T1D is characterized by a dialogue between the immune system and pancreatic β-cells. This dialogue is probably influenced by polymorphisms in genes expressed at the β-cell and/or immune system level, leading to inadequate responses to environmental cues such as viral infections. Further studies are needed to clarify how these disease-associated variants affect pancreatic β-cell responses to inflammation and the subsequent triggering of autoimmune responses and progressive β-cell loss.
Collapse
Affiliation(s)
- I Santin
- Laboratory of Experimental Medicine, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium.
| | | |
Collapse
|
202
|
New insights into the catalytic mechanism of histidine phosphatases revealed by a functionally essential arginine residue within the active site of the Sts phosphatases. Biochem J 2013; 453:27-35. [PMID: 23565972 DOI: 10.1042/bj20121769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sts (suppressor of T-cell receptor signalling)-1 and Sts-2 are HPs (histidine phosphatases) that negatively regulate TCR (T-cell receptor) signalling pathways, including those involved in cytokine production. HPs play key roles in such varied biological processes as metabolism, development and intracellular signalling. They differ considerably in their primary sequence and substrate specificity, but possess a catalytic core formed by an invariant quartet of active-site residues. Two histidine and two arginine residues cluster together within the HP active site and are thought to participate in a two-step dephosphorylation reaction. To date there has been little insight into any additional residues that might play an important functional role. In the present study, we identify and characterize an additional residue within the Sts phosphatases (Sts-1 Arg383 or Sts-2 Arg369) that is critical for catalytic activity and intracellular function. Mutation of Sts-1 Arg383 to an alanine residue compromises the enzyme's activity and renders Sts-1 unable to suppress TCR-induced cytokine induction. Of the multiple amino acids substituted for Arg383, only lysine partially rescues the catalytic activity of Sts-1. Although Sts-1 Arg383 is conserved in all Sts homologues, it is only conserved in one of the two sub-branches of HPs. The results of the present study highlight an essential role for Sts-1 phosphatase activity in regulating T-cell activation and add a new dimension of complexity to our understanding of HP catalytic activity.
Collapse
|
203
|
Östensson M, Montén C, Bacelis J, Gudjonsdottir AH, Adamovic S, Ek J, Ascher H, Pollak E, Arnell H, Browaldh L, Agardh D, Wahlström J, Nilsson S, Torinsson-Naluai Å. A possible mechanism behind autoimmune disorders discovered by genome-wide linkage and association analysis in celiac disease. PLoS One 2013; 8:e70174. [PMID: 23936387 PMCID: PMC3732286 DOI: 10.1371/journal.pone.0070174] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/14/2013] [Indexed: 12/30/2022] Open
Abstract
Celiac disease is a common autoimmune disorder characterized by an intestinal inflammation triggered by gluten, a storage protein found in wheat, rye and barley. Similar to other autoimmune diseases such as type 1 diabetes, psoriasis and rheumatoid arthritis, celiac disease is the result of an immune response to self-antigens leading to tissue destruction and production of autoantibodies. Common diseases like celiac disease have a complex pattern of inheritance with inputs from both environmental as well as additive and non-additive genetic factors. In the past few years, Genome Wide Association Studies (GWAS) have been successful in finding genetic risk variants behind many common diseases and traits. To complement and add to the previous findings, we performed a GWAS including 206 trios from 97 nuclear Swedish and Norwegian families affected with celiac disease. By stratifying for HLA-DQ, we identified a new genome-wide significant risk locus covering the DUSP10 gene. To further investigate the associations from the GWAS we performed pathway analyses and two-locus interaction analyses. These analyses showed an over-representation of genes involved in type 2 diabetes and identified a set of candidate mechanisms and genes of which some were selected for mRNA expression analysis using small intestinal biopsies from 98 patients. Several genes were expressed differently in the small intestinal mucosa from patients with celiac autoimmunity compared to intestinal mucosa from control patients. From top-scoring regions we identified susceptibility genes in several categories: 1) polarity and epithelial cell functionality; 2) intestinal smooth muscle; 3) growth and energy homeostasis, including proline and glutamine metabolism; and finally 4) innate and adaptive immune system. These genes and pathways, including specific functions of DUSP10, together reveal a new potential biological mechanism that could influence the genesis of celiac disease, and possibly also other chronic disorders with an inflammatory component.
Collapse
Affiliation(s)
- Malin Östensson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Caroline Montén
- Diabetes and Celiac Disease Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Jonas Bacelis
- Institute of Biomedicine, Department of Medical and Clinical Genetics, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Audur H. Gudjonsdottir
- Queen Silvia Children’s Hospital, Sahlgrenska Academy at the University of Gothenburg, Department of Pediatrics, Gothenburg, Sweden
| | - Svetlana Adamovic
- Institute of Biomedicine, Department of Medical and Clinical Genetics, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Johan Ek
- Buskerud Central Hospital, Department of Pediatrics, Drammen, Norway
| | - Henry Ascher
- Sahlgrenska Academy at the University of Gothenburg, Department of Public Health and Community Medicine, Unit of Social Medicine, Gothenburg, Sweden
| | - Elisabet Pollak
- Institute of Biomedicine, Department of Medical and Clinical Genetics, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Henrik Arnell
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Karolinska University Hospital and Division of Pediatrics, CLINTEC, Karolinska Institutet, Stockholm, Sweden
| | - Lars Browaldh
- Department of Clinical Science and Education, Karolinska Institutet Sodersjukhuset, Stockholm, Sweden
| | - Daniel Agardh
- Diabetes and Celiac Disease Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Jan Wahlström
- Institute of Biomedicine, Department of Medical and Clinical Genetics, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Staffan Nilsson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Åsa Torinsson-Naluai
- Institute of Biomedicine, Department of Medical and Clinical Genetics, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Systems Biology Research Centre, Tumor Biology, School of Life Sciences University of Skövde, Skövde, Sweden
- * E-mail:
| |
Collapse
|
204
|
Sams A, Hawks J. Patterns of population differentiation and natural selection on the celiac disease background risk network. PLoS One 2013; 8:e70564. [PMID: 23936230 PMCID: PMC3729812 DOI: 10.1371/journal.pone.0070564] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 06/24/2013] [Indexed: 12/20/2022] Open
Abstract
Celiac disease is a common small intestinal inflammatory condition induced by wheat gluten and related proteins from rye and barley. Left untreated, the clinical presentation of CD can include failure to thrive, malnutrition, and distension in juveniles. The disease can additionally lead to vitamin deficiencies, anemia, and osteoporosis. Therefore, CD potentially negatively affected fitness in past populations utilizing wheat, barley, and rye. Previous analyses of CD risk variants have uncovered evidence for positive selection on some of these loci. These studies also suggest the possibility that risk for common autoimmune conditions such as CD may be the result of positive selection on immune related loci in the genome to fight infection. Under this evolutionary scenario, disease phenotypes may be a trade-off from positive selection on immunity. If this hypothesis is generally true, we can expect to find a signal of natural selection when we survey across the network of loci known to influence CD risk. This study examines the non-HLA autosomal network of gene loci associated with CD risk in Europe. We reject the null hypothesis of neutrality on this network of CD risk loci. Additionally, we can localize evidence of selection in time and space by adding information from the genome of the Tyrolean Iceman. While we can show significant differentiation between continental regions across the CD network, the pattern of evidence is not consistent with primarily recent (Holocene) selection across this network in Europe. Further localization of ancient selection on this network may illuminate the ecological pressures acting on the immune system during this critically interesting phase of our evolution.
Collapse
Affiliation(s)
- Aaron Sams
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| | | |
Collapse
|
205
|
Teruel M, McKinney C, Balsa A, Pascual-Salcedo D, Rodriguez-Rodriguez L, Ortiz AM, Gómez-Vaquero C, González-Gay MA, Smith M, Witte T, Merriman T, Lie BA, Martin J. Association of CD247 polymorphisms with rheumatoid arthritis: a replication study and a meta-analysis. PLoS One 2013; 8:e68295. [PMID: 23861880 PMCID: PMC3702579 DOI: 10.1371/journal.pone.0068295] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 05/28/2013] [Indexed: 11/18/2022] Open
Abstract
Given the role of CD247 in the response of the T cells, its entailment in autoimmune diseases and in order to better clarify the role of this gene in RA susceptibility, we aimed to analyze CD247 gene variants previously associated with other autoimmune diseases (rs1052237, rs2056626 and rs864537) in a large independent European Caucasian population. However, no evidence of association was found for the analyzed CD247 single-nucleotide polymorphisms (SNPs) with RA and with the presence/absence of anti-cyclic citrullinated polypeptide. We performed a meta-analysis including previously published GWAS data from the rs864537 variant, revealing an overall genome-wide significant association between this CD247 SNP and RA with anti-CCP (OR = 0.90, CI 95% = 0.87-0.93, Poverall = 2.1×10(-10)). Our results show for first time a GWAS-level association between this CD247 polymorphism and RA risk.
Collapse
Affiliation(s)
- María Teruel
- Instituto de Parasitología y Biomedicina López-Neyra, Granada, Spain.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
206
|
Abstract
Genetic studies in immune-mediated diseases have yielded a large number of disease-associated loci. Here we review the progress being made in 12 such diseases, for which 199 independently associated non-HLA loci have been identified by genome-wide association studies since 2007. It is striking that many of the loci are not unique to a single disease but shared between different immune-mediated diseases. The challenge now is to understand how the unique and shared genetic factors can provide insight into the underlying disease biology. We annotated disease-associated variants using the Encyclopedia of DNA Elements (ENCODE) database and demonstrate that, of the predisposing disease variants, the majority have the potential to be regulatory. We also demonstrate that many of these variants affect the expression of nearby genes. Furthermore, we summarize results from the Immunochip, a custom array, which allows a detailed comparison between five of the diseases that have so far been analyzed using this platform.
Collapse
Affiliation(s)
- Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands;
| | | |
Collapse
|
207
|
Ochoa E, Iriondo M, Bielsa A, Ruiz-Irastorza G, Estonba A, Zubiaga AM. Thrombotic antiphospholipid syndrome shows strong haplotypic association with SH2B3-ATXN2 locus. PLoS One 2013; 8:e67897. [PMID: 23844121 PMCID: PMC3701057 DOI: 10.1371/journal.pone.0067897] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 05/22/2013] [Indexed: 01/11/2023] Open
Abstract
Background Thrombotic antiphospholipid syndrome is defined as a complex form of thrombophilia that is developed by a fraction of antiphospholipid antibody (aPLA) carriers. Little is known about the genetic risk factors involved in thrombosis development among aPLA carriers. Methods To identify new loci conferring susceptibility to thrombotic antiphospholipid syndrome, a two-stage genotyping strategy was performed. In stage one, 19,000 CNV loci were genotyped in 14 thrombotic aPLA+ patients and 14 healthy controls by array-CGH. In stage two, significant CNV loci were fine-mapped in a larger cohort (85 thrombotic aPLA+, 100 non-thrombotic aPLA+ and 569 healthy controls). Results Array-CGH and fine-mapping analysis led to the identification of 12q24.12 locus as a new susceptibility locus for thrombotic APS. Within this region, a TAC risk haplotype comprising one SNP in SH2B3 gene (rs3184504) and two SNPs in ATXN2 gene (rs10774625 and rs653178) exhibited the strongest association with thrombotic antiphospholipid syndrome (p-value = 5,9 × 10−4 OR 95% CI 1.84 (1.32–2.55)). Conclusion The presence of a TAC risk haplotype in ATXN2-SH2B3 locus may contribute to increased thrombotic risk in aPLA carriers.
Collapse
Affiliation(s)
- Eguzkine Ochoa
- Department of Genetics, Physical Anthropology and Animal Physiology. School of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Mikel Iriondo
- Department of Genetics, Physical Anthropology and Animal Physiology. School of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ana Bielsa
- Autoimmune Disease Research Unit, Service of Internal Medicine, Hospital de Cruces, University of the Basque Country (UPV/EHU), Barakaldo, Spain
| | - Guillermo Ruiz-Irastorza
- Autoimmune Disease Research Unit, Service of Internal Medicine, Hospital de Cruces, University of the Basque Country (UPV/EHU), Barakaldo, Spain
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology. School of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ana M. Zubiaga
- Department of Genetics, Physical Anthropology and Animal Physiology. School of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
- * E-mail:
| |
Collapse
|
208
|
Impact of coexistent celiac disease on phenotype and natural history of inflammatory bowel diseases. Am J Gastroenterol 2013; 108:1123-9. [PMID: 23419379 PMCID: PMC3845216 DOI: 10.1038/ajg.2013.20] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/15/2013] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Inflammatory bowel disease (IBD) and celiac disease are the two most common immune-mediated gastrointestinal diseases. There is limited knowledge regarding the course of IBD in those with coexisting celiac disease. We conducted this study to determine whether patients with coexisting celiac disease present a unique phenotype of IBD and to examine the frequency of co-occurrence of celiac disease and IBD in comparison with other autoimmune disorders. METHODS This was a case-control study performed at two tertiary referral centers. Cases comprised of patients with known diagnoses of celiac disease and IBD. Two random IBD controls without celiac disease were selected for each case after matching for IBD type. Disease phenotype and natural history for both Crohn's disease (CD) and ulcerative colitis (UC) were noted from medical record review, and were compared between IBD patients with and without celiac disease. RESULTS We identified a total of 51 patients with IBD (22 UC, 1 indeterminate colitis, 28 CD) and celiac disease. There was no significant difference in the age, gender, or ethnicity between celiac-IBD and controls. Pancolitis was more common in celiac-UC patients as compared with controls (odds ratio (OR) 3.30, 95% confidence interval (CI) 1.05-21.50). There was also a trend toward increased use of immunomodulators (IMMs) among celiac-UC patients than in non-celiac UC controls (OR 2.83, 95% CI 0.95-8.48). No phenotypic differences were found in celiac-CD patients. There were no significant differences in IBD-related medication usage, hospitalizations, or surgeries. CONCLUSIONS Patients with UC and celiac disease were more likely to have pancolitis and had a trend toward greater use of IMMs. Coexisting celiac disease did not influence natural history of CD.
Collapse
|
209
|
Stanford SM, Maestre MF, Campbell AM, Bartok B, Kiosses WB, Boyle DL, Arnett HA, Mustelin T, Firestein GS, Bottini N. Protein tyrosine phosphatase expression profile of rheumatoid arthritis fibroblast-like synoviocytes: a novel role of SH2 domain-containing phosphatase 2 as a modulator of invasion and survival. ACTA ACUST UNITED AC 2013; 65:1171-80. [PMID: 23335101 DOI: 10.1002/art.37872] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 01/10/2013] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The fibroblast-like synoviocytes (FLS) in the synovial intimal lining of the joint are key mediators of inflammation and joint destruction in rheumatoid arthritis (RA). In RA, these cells aggressively invade the extracellular matrix, producing cartilage-degrading proteases and inflammatory cytokines. The behavior of FLS is controlled by multiple interconnected signal transduction pathways involving reversible phosphorylation of proteins on tyrosine residues. However, little is known about the role of the protein tyrosine phosphatases (PTPs) in FLS function. This study was undertaken to explore the expression of all of the PTP genes (the PTPome) in FLS. METHODS A comparative screening of the expression of the PTPome in FLS from patients with RA and patients with osteoarthritis (OA) was conducted. The functional effect on RA FLS of SH2 domain-containing phosphatase 2 (SHP-2), a PTP that was up-regulated in RA, was then analyzed by knockdown using cell-permeable antisense oligonucleotides. RESULTS PTPN11 was overexpressed in RA FLS compared to OA FLS. Knockdown of PTPN11, which encodes SHP-2, reduced the invasion, migration, adhesion, spreading, and survival of RA FLS. Additionally, signaling in response to growth factors and inflammatory cytokines was impaired by SHP-2 knockdown. RA FLS that were deficient in SHP-2 exhibited decreased activation of focal adhesion kinase and mitogen-activated protein kinases. CONCLUSION These findings indicate that SHP-2 has a novel role in mediating human FLS function and suggest that it promotes the invasiveness and survival of RA FLS. Further investigation may reveal SHP-2 to be a candidate therapeutic target for RA.
Collapse
|
210
|
Chatzikyriakidou A, Voulgari PV, Lambropoulos A, Drosos AA. Genetics in rheumatoid arthritis beyond HLA genes: what meta-analyses have shown? Semin Arthritis Rheum 2013; 43:29-38. [PMID: 23768941 DOI: 10.1016/j.semarthrit.2012.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 11/28/2012] [Accepted: 12/06/2012] [Indexed: 01/15/2023]
Abstract
OBJECTIVE Rheumatoid arthritis (RA) is a complex disorder with many genetic and environmental factors to account for disease susceptibility. Individual genetic association studies usually suffer from small sample size leading to biased results of polymorphisms association with RA liability. Therefore, meta-analyses seem to resolve this limitation, up to a point, increasing the power of statistical analyses. In this review, we summarize the current knowledge of non-HLA genetic factors contributing to RA predisposition based on meta-analyses. METHODS Using the key words: rheumatoid arthritis, meta-analysis, and polymorphism, we searched the PubMed database for the associated articles. Up to the middle of November 2012, seventy-nine articles fulfilled the criteria and highlighted the current findings on the genetic factors contributing to RA susceptibility. RESULTS The association with RA was confirmed for 32 gene polymorphisms, being population specific in some cases. However, meta-analyses did not confirm an association in case of 16 gene variants, previously studied in individual studies for their association with RA. CONCLUSIONS The use of bioinformatics tools and functional studies of the summarized implicated genes in RA pathogenesis could shed light on the molecular pathways related to the disorder, helping to the development of new drug targets for a better treatment of RA.
Collapse
Affiliation(s)
- Anthoula Chatzikyriakidou
- Laboratory of General Biology and Genetics, Medical School, Aristotle University of Thessaloniki, Greece
| | | | | | | |
Collapse
|
211
|
Solovieff N, Cotsapas C, Lee PH, Purcell SM, Smoller JW. Pleiotropy in complex traits: challenges and strategies. Nat Rev Genet 2013; 14:483-95. [PMID: 23752797 DOI: 10.1038/nrg3461] [Citation(s) in RCA: 699] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies have identified many variants that each affects multiple traits, particularly across autoimmune diseases, cancers and neuropsychiatric disorders, suggesting that pleiotropic effects on human complex traits may be widespread. However, systematic detection of such effects is challenging and requires new methodologies and frameworks for interpreting cross-phenotype results. In this Review, we discuss the evidence for pleiotropy in contemporary genetic mapping studies, new and established analytical approaches to identifying pleiotropic effects, sources of spurious cross-phenotype effects and study design considerations. We also outline the molecular and clinical implications of such findings and discuss future directions of research.
Collapse
Affiliation(s)
- Nadia Solovieff
- Center for Human Genetics Research, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
| | | | | | | | | |
Collapse
|
212
|
Martin JE, Assassi S, Diaz-Gallo LM, Broen JC, Simeon CP, Castellvi I, Vicente-Rabaneda E, Fonollosa V, Ortego-Centeno N, González-Gay MA, Espinosa G, Carreira P, Camps M, Sabio JM, D'alfonso S, Vonk MC, Voskuyl AE, Schuerwegh AJ, Kreuter A, Witte T, Riemekasten G, Hunzelmann N, Airo P, Beretta L, Scorza R, Lunardi C, Van Laar J, Chee MM, Worthington J, Herrick A, Denton C, Fonseca C, Tan FK, Arnett F, Zhou X, Reveille JD, Gorlova O, Koeleman BPC, Radstake TRDJ, Vyse T, Mayes MD, Alarcón-Riquelme ME, Martin J. A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci. Hum Mol Genet 2013; 22:4021-9. [PMID: 23740937 DOI: 10.1093/hmg/ddt248] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Systemic sclerosis (SSc) and systemic lupus erythematosus (SLE) are two archetypal systemic autoimmune diseases which have been shown to share multiple genetic susceptibility loci. In order to gain insight into the genetic basis of these diseases, we performed a pan-meta-analysis of two genome-wide association studies (GWASs) together with a replication stage including additional SSc and SLE cohorts. This increased the sample size to a total of 21,109 (6835 cases and 14,274 controls). We selected for replication 19 SNPs from the GWAS data. We were able to validate KIAA0319L (P = 3.31 × 10(-11), OR = 1.49) as novel susceptibility loci for SSc and SLE. Furthermore, we also determined that the previously described SLE susceptibility loci PXK (P = 3.27 × 10(-11), OR = 1.20) and JAZF1 (P = 1.11 × 10(-8), OR = 1.13) are shared with SSc. Supporting these new discoveries, we observed that KIAA0319L was overexpressed in peripheral blood cells of SSc and SLE patients compared with healthy controls. With these, we add three (KIAA0319L, PXK and JAZF1) and one (KIAA0319L) new susceptibility loci for SSc and SLE, respectively, increasing significantly the knowledge of the genetic basis of autoimmunity.
Collapse
|
213
|
Stringaris A. Here/in this issue and there/abstract thinking: gene effects cross the boundaries of psychiatric disorders. J Am Acad Child Adolesc Psychiatry 2013; 52:557-8. [PMID: 23702441 PMCID: PMC7614276 DOI: 10.1016/j.jaac.2013.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 03/27/2013] [Indexed: 10/26/2022]
|
214
|
Herráez DL, Martínez-Bueno M, Riba L, de la Torre IG, Sacnún M, Goñi M, Berbotto GA, Paira S, Musuruana JL, Graf CE, Alvarellos AJ, Messina OD, Babini AM, Strusberg I, Marcos JC, Scherbarth H, Spindler AJ, Quinteros A, Toloza SMA, Moreno JLC, Catoggio LJ, Tate G, Eimon A, Citera G, Catalán Pellet A, Nasswetter GG, Cardiel MH, Miranda P, Ballesteros F, Esquivel-Valerio JA, Maradiaga-Ceceña MA, Acevedo-Vásquez EM, García García C, Tusié-Luna T, Pons-Estel BA, Alarcón-Riquelme ME. Rheumatoid Arthritis in Latin Americans Enriched for Amerindian Ancestry Is Associated With Loci in Chromosomes 1, 12, and 13, and the HLA Class II Region. ACTA ACUST UNITED AC 2013; 65:1457-67. [DOI: 10.1002/art.37923] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 02/26/2013] [Indexed: 02/06/2023]
Affiliation(s)
- David López Herráez
- Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigaciones Oncológicas, Granada, Spain
| | - Manuel Martínez-Bueno
- Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigaciones Oncológicas, Granada, Spain
| | - Laura Riba
- Instituto de Investigaciones Biomédicas de la Universidad Nacional Autónoma de México and Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | | | - Mario Goñi
- Instituto Lucha Antipoliomielítica de Rosario, Rosario, Argentina
| | | | | | | | | | | | | | | | | | - Juan Carlos Marcos
- Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigaciones Oncológicas, Granada, Spain
| | - Hugo Scherbarth
- Hospital Interzonal General de Agudos Oscar E. Alende, Mar del Plata, Argentina
| | | | - Ana Quinteros
- Fundación Instituto para la Promoción de la Salud y la Educación, San Miguel de Tucumán, Argentina
| | - Sergio M. A. Toloza
- Hospital Interzonal San Juan Bautista, San Fernando del Valle de Catamarca, Argentina
| | | | | | | | - Alicia Eimon
- Centro de Educación Médica e Investigaciones Clínicas, Buenos Aires, Argentina
| | - Gustavo Citera
- Instituto de Rehabilitación Psicofísica, Ciudad Autónoma de Buenos Aires, Argentina
| | | | | | - Mario H. Cardiel
- Unidad de Investigación “Dr. Mario Alvizouri Muñoz,” Hospital General “Dr. Miguel Silva,” Secretaría de Salud de Michoacán, Morelia, Michoacán, Mexico
| | | | | | - Jorge A. Esquivel-Valerio
- Hospital Universitario Dr. José Eleuterio González and Universidad Autonoma de Nuevo León, Monterrey, Mexico
| | | | - Eduardo M. Acevedo-Vásquez
- Hospital Nacional Guillermo Almenara Irigoyen EsSalud and Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | - Teresa Tusié-Luna
- Instituto de Investigaciones Biomédicas de la Universidad Nacional Autónoma de México and Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Marta E. Alarcón-Riquelme
- Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigaciones Oncológicas, Granada, Spain, and Oklahoma Medical Research Foundation, Oklahoma City
| | | |
Collapse
|
215
|
Deng FY, Lei SF, Zhu H, Zhang YH, Zhang ZL. Integrative analyses for functional mechanisms underlying associations for rheumatoid arthritis. J Rheumatol 2013; 40:1063-8. [PMID: 23678157 DOI: 10.3899/jrheum.121119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
OBJECTIVE Extensive association analyses including genome-wide association studies (GWAS) and powerful metaanalysis studies have identified a long list of loci associated with rheumatoid arthritis (RA) in very large populations, but most of them established statistical associations of genetic markers and RA only at the DNA level, without supporting evidence of functional relevance. Our study serves as a trial to detect the functional mechanisms underlying associations for RA by searching publicly available datasets and results. METHODS Based on publicly available datasets and results, we performed integrative analyses (gene relationships across implicated loci analysis, differential gene expression analysis, and functional annotation clustering analysis) and combined them with the expression quantitative trait locus (eQTL) results to dissect functional mechanisms underlying the associations for RA. RESULTS By searching 2 GWAS, Integrator and PheGenI, we selected 98 RA association results (p < 10(-5)). Among these associations, we found that 8 single-nucleotide polymorphisms (SNP; rs1600249, rs2736340, rs3093023, rs3093024, rs4810485, rs615672, rs660895, and rs9272219) serve as cis-effect regulators of the corresponding eQTL genes (BLK and CD4 in non-HLA region; CCR6, HLA-DQA1, and HLA-DQB1 in HLA region) that also were differentially expressed in RA-related cell groups. These 5 genes are closely related with immune response in function. CONCLUSION Our results showed the functional mechanisms underlying the associations of 8 SNP and the corresponding genes. This study is an example of mining publicly available datasets and results in validation of significant disease-association results. Using public data resources for integrative analyses may provide insights into the molecular genetic mechanisms underlying human diseases.
Collapse
Affiliation(s)
- Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, and the Department of Epidemiology, School of Public Health, Soochow University, Suzhou, Jiangsu, China
| | | | | | | | | |
Collapse
|
216
|
He X, Fuller C, Song Y, Meng Q, Zhang B, Yang X, Li H. Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS. Am J Hum Genet 2013; 92:667-80. [PMID: 23643380 PMCID: PMC3644637 DOI: 10.1016/j.ajhg.2013.03.022] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 03/07/2013] [Accepted: 03/25/2013] [Indexed: 12/26/2022] Open
Abstract
Genetic mapping of complex diseases to date depends on variations inside or close to the genes that perturb their activities. A strong body of evidence suggests that changes in gene expression play a key role in complex diseases and that numerous loci perturb gene expression in trans. The information in trans variants, however, has largely been ignored in the current analysis paradigm. Here we present a statistical framework for genetic mapping by utilizing collective information in both cis and trans variants. We reason that for a disease-associated gene, any genetic variation that perturbs its expression is also likely to influence the disease risk. Thus, the expression quantitative trait loci (eQTL) of the gene, which constitute a unique "genetic signature," should overlap significantly with the set of loci associated with the disease. We translate this idea into a computational algorithm (named Sherlock) to search for gene-disease associations from GWASs, taking advantage of independent eQTL data. Application of this strategy to Crohn disease and type 2 diabetes predicts a number of genes with possible disease roles, including several predictions supported by solid experimental evidence. Importantly, predicted genes are often implicated by multiple trans eQTL with moderate associations. These genes are far from any GWAS association signals and thus cannot be identified from the GWAS alone. Our approach allows analysis of association data from a new perspective and is applicable to any complex phenotype. It is readily generalizable to molecular traits other than gene expression, such as metabolites, noncoding RNAs, and epigenetic modifications.
Collapse
Affiliation(s)
- Xin He
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
- Lane Center of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Chris K. Fuller
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Yi Song
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Qingying Meng
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
| |
Collapse
|
217
|
Abstract
BACKGROUND Findings from family and twin studies suggest that genetic contributions to psychiatric disorders do not in all cases map to present diagnostic categories. We aimed to identify specific variants underlying genetic effects shared between the five disorders in the Psychiatric Genomics Consortium: autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia. METHODS We analysed genome-wide single-nucleotide polymorphism (SNP) data for the five disorders in 33,332 cases and 27,888 controls of European ancestory. To characterise allelic effects on each disorder, we applied a multinomial logistic regression procedure with model selection to identify the best-fitting model of relations between genotype and phenotype. We examined cross-disorder effects of genome-wide significant loci previously identified for bipolar disorder and schizophrenia, and used polygenic risk-score analysis to examine such effects from a broader set of common variants. We undertook pathway analyses to establish the biological associations underlying genetic overlap for the five disorders. We used enrichment analysis of expression quantitative trait loci (eQTL) data to assess whether SNPs with cross-disorder association were enriched for regulatory SNPs in post-mortem brain-tissue samples. FINDINGS SNPs at four loci surpassed the cutoff for genome-wide significance (p<5×10(-8)) in the primary analysis: regions on chromosomes 3p21 and 10q24, and SNPs within two L-type voltage-gated calcium channel subunits, CACNA1C and CACNB2. Model selection analysis supported effects of these loci for several disorders. Loci previously associated with bipolar disorder or schizophrenia had variable diagnostic specificity. Polygenic risk scores showed cross-disorder associations, notably between adult-onset disorders. Pathway analysis supported a role for calcium channel signalling genes for all five disorders. Finally, SNPs with evidence of cross-disorder association were enriched for brain eQTL markers. INTERPRETATION Our findings show that specific SNPs are associated with a range of psychiatric disorders of childhood onset or adult onset. In particular, variation in calcium-channel activity genes seems to have pleiotropic effects on psychopathology. These results provide evidence relevant to the goal of moving beyond descriptive syndromes in psychiatry, and towards a nosology informed by disease cause. FUNDING National Institute of Mental Health.
Collapse
|
218
|
Liu L, Zhang D, Liu H, Arendt C. Robust methods for population stratification in genome wide association studies. BMC Bioinformatics 2013; 14:132. [PMID: 23601181 PMCID: PMC3637636 DOI: 10.1186/1471-2105-14-132] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 03/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background Genome-wide association studies can provide novel insights into diseases of interest, as well as to the responsiveness of an individual to specific treatments. In such studies, it is very important to correct for population stratification, which refers to allele frequency differences between cases and controls due to systematic ancestry differences. Population stratification can cause spurious associations if not adjusted properly. The principal component analysis (PCA) method has been relied upon as a highly useful methodology to adjust for population stratification in these types of large-scale studies. Recently, the linear mixed model (LMM) has also been proposed to account for family structure or cryptic relatedness. However, neither of these approaches may be optimal in properly correcting for sample structures in the presence of subject outliers. Results We propose to use robust PCA combined with k-medoids clustering to deal with population stratification. This approach can adjust for population stratification for both continuous and discrete populations with subject outliers, and it can be considered as an extension of the PCA method and the multidimensional scaling (MDS) method. Through simulation studies, we compare the performance of our proposed methods with several widely used stratification methods, including PCA and MDS. We show that subject outliers can greatly influence the analysis results from several existing methods, while our proposed robust population stratification methods perform very well for both discrete and admixed populations with subject outliers. We illustrate the new method using data from a rheumatoid arthritis study. Conclusions We demonstrate that subject outliers can greatly influence the analysis result in GWA studies, and propose robust methods for dealing with population stratification that outperform existing population stratification methods in the presence of subject outliers.
Collapse
Affiliation(s)
- Li Liu
- Department of Biostatistics and Programming, Mail Stop 55C-305A, 55 Corporate Drive, Sanofi, Bridgewater, NJ 08807, USA.
| | | | | | | |
Collapse
|
219
|
Suzuki T, Ikari K, Yano K, Inoue E, Toyama Y, Taniguchi A, Yamanaka H, Momohara S. PADI4 and HLA-DRB1 are genetic risks for radiographic progression in RA patients, independent of ACPA status: results from the IORRA cohort study. PLoS One 2013; 8:e61045. [PMID: 23577190 PMCID: PMC3620057 DOI: 10.1371/journal.pone.0061045] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 03/05/2013] [Indexed: 12/23/2022] Open
Abstract
Introduction Rheumatoid arthritis (RA) is a systemic, chronic inflammatory disease influenced by both genetic and environmental factors, leading to joint destruction and functional impairment. Recently, a large-scaled GWAS meta-analysis using more than 37,000 Japanese samples were conducted and 13 RA susceptibility loci were identified. However, it is not clear whether these loci have significant impact on joint destruction or not. This is the first study focused on the 13 loci to investigate independent genetic risk factors for radiographic progression in the first five years from onset of RA. Methods Sharp/van der Heijde score of hands at 5-year disease duration, which represents joint damage, were measured retrospectively and used as an outcome variable in 865 Japanese RA patients. Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by the Japanese GWAS meta-analysis, including HLA-DRB1 (shared epitope, SE), rs2240340 (PADI4), rs2230926 (TNFAIP3), rs3093024 (CCR6), rs11900673 (B3GNT2), rs2867461 (ANXA3), rs657075 (CSF2), rs12529514 (CD83), rs2233434 (NFKBIE), rs10821944 (ARID5B), rs3781913 (PDE2A-ARAP1), rs2841277 (PLD4) and rs2847297 (PTPN2). These putative genetic risk factors were assessed by a stepwise multiple regression analysis adjusted for possible non-genetic risk factors: autoantibody positivity (anti-citrullinated peptide antibody [ACPA] and rheumatoid factor), history of smoking, gender and age at disease onset. Results The number of SE alleles (P = 0.002) and risk alleles of peptidyl arginine deiminase type IV gene (PADI4, P = 0.04) had significant impact on progressive joint destruction, as well as following non-genetic factors: ACPA positive (P = 0.0006), female sex (P = 0.006) and younger age of onset (P = 0.02). Conclusions In the present study, we found that PADI4 risk allele and HLA-DRB1 shared epitope are independent genetic risks for radiographic progression in Japanese rheumatoid arthritis patients. The results of this study give important knowledge of the risks on progressive joint damage in RA patients.
Collapse
Affiliation(s)
- Taku Suzuki
- Institute of Rheumatology, Tokyo Women’s Medical University, Shinjuku, Tokyo, Japan
- Department of Orthopaedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women’s Medical University, Shinjuku, Tokyo, Japan
- * E-mail:
| | - Koichiro Yano
- Institute of Rheumatology, Tokyo Women’s Medical University, Shinjuku, Tokyo, Japan
| | - Eisuke Inoue
- Institute of Rheumatology, Tokyo Women’s Medical University, Shinjuku, Tokyo, Japan
| | - Yoshiaki Toyama
- Department of Orthopaedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Atsuo Taniguchi
- Institute of Rheumatology, Tokyo Women’s Medical University, Shinjuku, Tokyo, Japan
| | - Hisashi Yamanaka
- Institute of Rheumatology, Tokyo Women’s Medical University, Shinjuku, Tokyo, Japan
| | - Shigeki Momohara
- Institute of Rheumatology, Tokyo Women’s Medical University, Shinjuku, Tokyo, Japan
| |
Collapse
|
220
|
Common risk alleles for inflammatory diseases are targets of recent positive selection. Am J Hum Genet 2013; 92:517-29. [PMID: 23522783 DOI: 10.1016/j.ajhg.2013.03.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/13/2012] [Accepted: 03/01/2013] [Indexed: 11/22/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified hundreds of loci harboring genetic variation influencing inflammatory-disease susceptibility in humans. It has been hypothesized that present day inflammatory diseases may have arisen, in part, due to pleiotropic effects of host resistance to pathogens over the course of human history, with significant selective pressures acting to increase host resistance to pathogens. The extent to which genetic factors underlying inflammatory-disease susceptibility has been influenced by selective processes can now be quantified more comprehensively than previously possible. To understand the evolutionary forces that have shaped inflammatory-disease susceptibility and to elucidate functional pathways affected by selection, we performed a systems-based analysis to integrate (1) published GWASs for inflammatory diseases, (2) a genome-wide scan for signatures of positive selection in a population of European ancestry, (3) functional genomics data comprised of protein-protein interaction networks, and (4) a genome-wide expression quantitative trait locus (eQTL) mapping study in peripheral blood mononuclear cells (PBMCs). We demonstrate that loci for inflammatory-disease susceptibility are enriched for genomic signatures of recent positive natural selection, with selected loci forming a highly interconnected protein-protein interaction network. Further, we identify 21 loci for inflammatory-disease susceptibility that display signatures of recent positive selection, of which 13 also show evidence of cis-regulatory effects on genes within the associated locus. Thus, our integrated analyses highlight a set of susceptibility loci that might subserve a shared molecular function and has experienced selective pressure over the course of human history; today, these loci play a key role in influencing susceptibility to multiple different inflammatory diseases, in part through alterations of gene expression in immune cells.
Collapse
|
221
|
Evidence of new risk genetic factor to systemic lupus erythematosus: the UBASH3A gene. PLoS One 2013; 8:e60646. [PMID: 23565265 PMCID: PMC3614928 DOI: 10.1371/journal.pone.0060646] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/01/2013] [Indexed: 11/18/2022] Open
Abstract
The ubiquitin associated and Src-homology 3 (SH3) domain containing A (UBASH3a) is a suppressor of T-cell receptor signaling, underscoring antigen presentation to T-cells as a critical shared mechanism of diseases pathogenesis. The aim of the present study was to determine whether the UBASH3a gene influence the susceptibility to systemic lupus erythematosus (SLE) in Caucasian populations. We evaluated five UBASH3a polymorphisms (rs2277798, rs2277800, rs9976767, rs13048049 and rs17114930), using TaqMan® allelic discrimination assays, in a discovery cohort that included 906 SLE patients and 1165 healthy controls from Spain. The SNPs that exhibit statistical significance difference were evaluated in a German replication cohort of 360 SLE patients and 379 healthy controls. The case-control analysis in the Spanish population showed a significant association between the rs9976767 and SLE (Pc = 9.9E-03 OR = 1.21 95%CI = 1.07–1.37) and a trend of association for the rs2277798 analysis (P = 0.09 OR = 0.9 95%CI = 0.79–1.02). The replication in a German cohort and the meta-analysis confirmed that the rs9976767 (Pc = 0.02; Pc = 2.4E-04, for German cohort and meta-analysis, respectively) and rs2277798 (Pc = 0.013; Pc = 4.7E-03, for German cohort and meta-analysis, respectively) UBASH3a variants are susceptibility factors for SLE. Finally, a conditional regression analysis suggested that the most likely genetic variation responsible for the association was the rs9976767 polymorphism. Our results suggest that UBASH3a gene plays a role in the susceptibility to SLE. Moreover, our study indicates that UBASH3a can be considered as a common genetic factor in autoimmune diseases.
Collapse
|
222
|
Takeuchi T, Suzuki K. CD247 variants and single-nucleotide polymorphisms observed in systemic lupus erythematosus patients. Rheumatology (Oxford) 2013; 52:1551-5. [DOI: 10.1093/rheumatology/ket119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
223
|
Abstract
Coeliac disease, an inflammatory disease of the small intestine, shares key features with autoimmune disorders, such as susceptibility genes, presence of autoantibodies and T cell-mediated destruction of specific cells. Strikingly, however, continuous exposure to the exogenous dietary antigen gluten and gluten-specific adaptive immunity are required to maintain immunopathology. These observations challenge the notion that autoimmunity requires adaptive immune activation towards self antigens. Using coeliac disease as an example, we propose that other exogenous factors might be identified as drivers of autoimmune processes, in particular when evidence for T cells with specificity for self antigens driving the disease is lacking.
Collapse
|
224
|
Lu Y, Chen H, Nikamo P, Qi Low H, Helms C, Seielstad M, Liu J, Bowcock AM, Stahle M, Liao W. Association of cardiovascular and metabolic disease genes with psoriasis. J Invest Dermatol 2013; 133:836-839. [PMID: 23190900 PMCID: PMC3570714 DOI: 10.1038/jid.2012.366] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yingchang Lu
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Haoyan Chen
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Pernilla Nikamo
- Unit of Dermatology and Venereology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Hui Qi Low
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Cynthia Helms
- Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA
| | - Mark Seielstad
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore; Institute for Human Genetics and Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Anne M Bowcock
- Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA
| | - Mona Stahle
- Unit of Dermatology and Venereology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA.
| |
Collapse
|
225
|
Volta U, Caio G, Tovoli F, De Giorgio R. Gut-liver axis: an immune link between celiac disease and primary biliary cirrhosis. Expert Rev Gastroenterol Hepatol 2013; 7:253-61. [PMID: 23445234 DOI: 10.1586/egh.13.5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The association between celiac disease and primary biliary cirrhosis is well established. The breakdown of gut-liver axis equilibrium plays a central role in the development of immune disorders involving the small bowel and liver. In celiac disease, immunologically active molecules generated from the cross-linking between tissue transglutaminase and food/bacterial antigens reach the liver through the portal circulation owing to the increased intestinal permeability. A molecular mimicry between bacterial antigens and the pyruvate dehydrogenase E2 component, recognized by antimitochondrial autoantibodies, may have a role in primary biliary cirrhosis pathogenesis. An aberrant intestinal T lymphocyte homing to the liver may contribute to trigger immune hepatic damage. Both celiac disease and primary biliary cirrhosis share several features, including a higher prevalence in females, autoimmune comorbidities and specific autoantibodies. Reciprocal screening for both diseases is recommended, as an early diagnosis with the appropriate treatment can improve the outcome of these patients.
Collapse
Affiliation(s)
- Umberto Volta
- Department of Medical & Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Italy.
| | | | | | | |
Collapse
|
226
|
Svendsen AJ, Kyvik KO, Houen G, Junker P, Christensen K, Christiansen L, Nielsen C, Skytthe A, Hjelmborg JV. On the origin of rheumatoid arthritis: the impact of environment and genes--a population based twin study. PLoS One 2013; 8:e57304. [PMID: 23468964 PMCID: PMC3585362 DOI: 10.1371/journal.pone.0057304] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/20/2013] [Indexed: 01/07/2023] Open
Abstract
Background Rheumatoid arthritis (RA) is an autoimmune disease with a complex origin. Previous studies have reported heritability estimates on RA at about 60%. Only 16% of the genetic background of the disease has been disclosed so far. The purpose of the present investigation was to provide an optimized estimate on the heritability of RA and to study the recurrence risk in a nationwide Caucasian twin population. Methods and Findings In a mail survey addressed to 56.707 twin individuals, RA was reported by 479 individuals, mean age 52 (range 16–73). Respondents underwent an interview and clinical examination. Ascertainment probability was 80%. RA was confirmed in 162 twin individuals yielding a prevalence at 0.37% (95% CI 0.31–0.43). The mean discordance time was 19 years (range 0–57). The concordance was 9.1% (95% CI 1.9 to 24.3) in MZ, 6.4% (95% CI 2.1 to 14.3) in DZss. The increased relative risk of attracting RA conditioned on having an affected cotwin compared to the background population risk was 24.6 to 35.4 in MZ twins and 17.3 to 31.6 in DZss twins. The correlation coefficients were 0.60 (0.33 to 0.78) in monozygotic (MZ) and 0.55 (0.33 to 0.72) in dizygotic same sexed (DZss) pairs. Twelve percent (95% CI 0–76%) of the phenotypic variance in the liability to RA was due to additive genetic effects, 50% (95% CI 0–72%) to shared environmental effects and 38% (95% CI 17–61%) to non-shared environmental effects. Conclusions This study emphasizes that family factors are important for the development of RA. Although genetic effectors are important, shared and non-shared environmental triggers and/or epigenetic stochastic events seem to be even more significant. However, it should be borne in mind that the genetic and non-genetic components may not be the same across disease subsets.
Collapse
Affiliation(s)
- Anders J Svendsen
- Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark.
| | | | | | | | | | | | | | | | | |
Collapse
|
227
|
Cortes A, Field J, Glazov EA, Hadler J, Stankovich J, Brown MA. Resequencing and fine-mapping of the chromosome 12q13-14 locus associated with multiple sclerosis refines the number of implicated genes. Hum Mol Genet 2013; 22:2283-92. [PMID: 23406874 DOI: 10.1093/hmg/ddt062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Multiple sclerosis (MS) is a common chronic inflammatory disease of the central nervous system. Susceptibility to the disease is affected by both environmental and genetic factors. Genetic factors include haplotypes in the histocompatibility complex (MHC) and over 50 non-MHC loci reported by genome-wide association studies. Amongst these, we previously reported polymorphisms in chromosome 12q13-14 with a protective effect in individuals of European descent. This locus spans 288 kb and contains 17 genes, including several candidate genes which have potentially significant pathogenic and therapeutic implications. In this study, we aimed to fine-map this locus. We have implemented a two-phase study: a variant discovery phase where we have used next-generation sequencing and two target-enrichment strategies [long-range polymerase chain reaction (PCR) and Nimblegen's solution phase hybridization capture] in pools of 25 samples; and a genotyping phase where we genotyped 712 variants in 3577 healthy controls and 3269 MS patients. This study confirmed the association (rs2069502, P = 9.9 × 10(-11), OR = 0.787) and narrowed down the locus of association to an 86.5 kb region. Although the study was unable to pinpoint the key-associated variant, we have identified a 42 (genotyped and imputed) single-nucleotide polymorphism haplotype block likely to harbour the causal variant. No evidence of association at previously reported low-frequency variants in CYP27B1 was observed. As part of the study we compared variant discovery performance using two target-enrichment strategies. We concluded that our pools enriched with Nimblegen's solution phase hybridization capture had better sensitivity to detect true variants than the pools enriched with long-range PCR, whilst specificity was better in the long-range PCR-enriched pools compared with solution phase hybridization capture enriched pools; this result has important implications for the design of future fine-mapping studies.
Collapse
Affiliation(s)
- Adrian Cortes
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Qld. 4102, Australia
| | | | | | | | | | | | | |
Collapse
|
228
|
Abstract
Investigators have made key advances in rheumatoid arthritis (RA) genetics in the past 10 years. Although genetic studies have had limited influence on clinical practice and drug discovery, they are currently generating testable hypotheses to explain disease pathogenesis. Firstly, we review here the major advances in identifying RA genetic susceptibility markers both within and outside of the MHC. Understanding how genetic variants translate into pathogenic mechanisms and ultimately into phenotypes remains a mystery for most of the polymorphisms that confer susceptibility to RA, but functional data are emerging. Interplay between environmental and genetic factors is poorly understood and in need of further investigation. Secondly, we review current knowledge of the role of epigenetics in RA susceptibility. Differences in the epigenome could represent one of the ways in which environmental exposures translate into phenotypic outcomes. The best understood epigenetic phenomena include post-translational histone modifications and DNA methylation events, both of which have critical roles in gene regulation. Epigenetic studies in RA represent a new area of research with the potential to answer unsolved questions.
Collapse
Affiliation(s)
- Sebastien Viatte
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
| | | | | |
Collapse
|
229
|
Immune-mediated disease genetics: the shared basis of pathogenesis. Trends Immunol 2013; 34:22-6. [DOI: 10.1016/j.it.2012.09.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 09/06/2012] [Accepted: 09/06/2012] [Indexed: 12/28/2022]
|
230
|
Yan Zhang E, Kong KF, Altman A. The yin and yang of protein kinase C-theta (PKCθ): a novel drug target for selective immunosuppression. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2013; 66:267-312. [PMID: 23433459 PMCID: PMC3903317 DOI: 10.1016/b978-0-12-404717-4.00006-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein kinase C-theta (PKCθ) is a protein kinase C (PKC) family member expressed predominantly in T lymphocytes, and extensive studies addressing its function have been conducted. PKCθ is the only T cell-expressed PKC that localizes selectively to the center of the immunological synapse (IS) following conventional T cell antigen stimulation, and this unique localization is essential for PKCθ-mediated downstream signaling. While playing a minor role in T cell development, early in vitro studies relying, among others, on the use of PKCθ-deficient (Prkcq(-/-)) T cells revealed that PKCθ is required for the activation and proliferation of mature T cells, reflecting its importance in activating the transcription factors nuclear factor kappa B, activator protein-1, and nuclear factor of activated T cells, as well as for the survival of activated T cells. Upon subsequent analysis of in vivo immune responses in Prkcq(-/-) mice, it became clear that PKCθ has a selective role in the immune system: it is required for experimental Th2- and Th17-mediated allergic and autoimmune diseases, respectively, and for alloimmune responses, but is dispensable for protective responses against pathogens and for graft-versus-leukemia responses. Surprisingly, PKCθ was recently found to be excluded from the IS of regulatory T cells and to negatively regulate their suppressive function. These attributes of PKCθ make it an attractive target for catalytic or allosteric inhibitors that are expected to selectively suppress harmful inflammatory and alloimmune responses without interfering with beneficial immunity to infections. Early progress in developing such drugs is being made, but additional studies on the role of PKCθ in the human immune system are urgently needed.
Collapse
Affiliation(s)
| | | | - Amnon Altman
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| |
Collapse
|
231
|
van der Harst P, Zhang W, Mateo Leach I, Rendon A, Verweij N, Sehmi J, Paul DS, Elling U, Allayee H, Li X, Radhakrishnan A, Tan ST, Voss K, Weichenberger CX, Albers CA, Al-Hussani A, Asselbergs FW, Ciullo M, Danjou F, Dina C, Esko T, Evans DM, Franke L, Gögele M, Hartiala J, Hersch M, Holm H, Hottenga JJ, Kanoni S, Kleber ME, Lagou V, Langenberg C, Lopez LM, Lyytikäinen LP, Melander O, Murgia F, Nolte IM, O'Reilly PF, Padmanabhan S, Parsa A, Pirastu N, Porcu E, Portas L, Prokopenko I, Ried JS, Shin SY, Tang CS, Teumer A, Traglia M, Ulivi S, Westra HJ, Yang J, Zhao JH, Anni F, Abdellaoui A, Attwood A, Balkau B, Bandinelli S, Bastardot F, Benyamin B, Boehm BO, Cookson WO, Das D, de Bakker PIW, de Boer RA, de Geus EJC, de Moor MH, Dimitriou M, Domingues FS, Döring A, Engström G, Eyjolfsson GI, Ferrucci L, Fischer K, Galanello R, Garner SF, Genser B, Gibson QD, Girotto G, Gudbjartsson DF, Harris SE, Hartikainen AL, Hastie CE, Hedblad B, Illig T, Jolley J, Kähönen M, Kema IP, Kemp JP, Liang L, Lloyd-Jones H, Loos RJF, Meacham S, Medland SE, Meisinger C, Memari Y, Mihailov E, Miller K, Moffatt MF, Nauck M, Novatchkova M, Nutile T, Olafsson I, Onundarson PT, Parracciani D, Penninx BW, Perseu L, Piga A, Pistis G, Pouta A, Puc U, Raitakari O, Ring SM, Robino A, Ruggiero D, Ruokonen A, Saint-Pierre A, Sala C, Salumets A, Sambrook J, Schepers H, Schmidt CO, Silljé HHW, Sladek R, Smit JH, Starr JM, Stephens J, Sulem P, Tanaka T, Thorsteinsdottir U, Tragante V, van Gilst WH, van Pelt LJ, van Veldhuisen DJ, Völker U, Whitfield JB, Willemsen G, Winkelmann BR, Wirnsberger G, Algra A, Cucca F, d'Adamo AP, Danesh J, Deary IJ, Dominiczak AF, Elliott P, Fortina P, Froguel P, Gasparini P, Greinacher A, Hazen SL, Jarvelin MR, Khaw KT, Lehtimäki T, Maerz W, Martin NG, Metspalu A, Mitchell BD, Montgomery GW, Moore C, Navis G, Pirastu M, Pramstaller PP, Ramirez-Solis R, Schadt E, Scott J, Shuldiner AR, Smith GD, Smith JG, Snieder H, Sorice R, Spector TD, Stefansson K, Stumvoll M, Tang WHW, Toniolo D, Tönjes A, Visscher PM, Vollenweider P, Wareham NJ, Wolffenbuttel BHR, Boomsma DI, Beckmann JS, Dedoussis GV, Deloukas P, Ferreira MA, Sanna S, Uda M, Hicks AA, Penninger JM, Gieger C, Kooner JS, Ouwehand WH, Soranzo N, Chambers JC. Seventy-five genetic loci influencing the human red blood cell. Nature 2012; 492:369-75. [PMID: 23222517 PMCID: PMC3623669 DOI: 10.1038/nature11677] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 10/15/2012] [Indexed: 11/09/2022]
Abstract
Anaemia is a chief determinant of global ill health, contributing to cognitive impairment, growth retardation and impaired physical capacity. To understand further the genetic factors influencing red blood cells, we carried out a genome-wide association study of haemoglobin concentration and related parameters in up to 135,367 individuals. Here we identify 75 independent genetic loci associated with one or more red blood cell phenotypes at P < 10(-8), which together explain 4-9% of the phenotypic variance per trait. Using expression quantitative trait loci and bioinformatic strategies, we identify 121 candidate genes enriched in functions relevant to red blood cell biology. The candidate genes are expressed preferentially in red blood cell precursors, and 43 have haematopoietic phenotypes in Mus musculus or Drosophila melanogaster. Through open-chromatin and coding-variant analyses we identify potential causal genetic variants at 41 loci. Our findings provide extensive new insights into genetic mechanisms and biological pathways controlling red blood cell formation and function.
Collapse
Affiliation(s)
- Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
232
|
Tsoi LC, Spain SL, Knight J, Ellinghaus E, Stuart PE, Capon F, Ding J, Li Y, Tejasvi T, Gudjonsson JE, Kang HM, Allen MH, McManus R, Novelli G, Samuelsson L, Schalkwijk J, Ståhle M, Burden AD, Smith CH, Cork MJ, Estivill X, Bowcock AM, Krueger GG, Weger W, Worthington J, Tazi-Ahnini R, Nestle FO, Hayday A, Hoffmann P, Winkelmann J, Wijmenga C, Langford C, Edkins S, Andrews R, Blackburn H, Strange A, Band G, Pearson RD, Vukcevic D, Spencer CCA, Deloukas P, Mrowietz U, Schreiber S, Weidinger S, Koks S, Kingo K, Esko T, Metspalu A, Lim HW, Voorhees JJ, Weichenthal M, Wichmann HE, Chandran V, Rosen CF, Rahman P, Gladman DD, Griffiths CEM, Reis A, Kere J, Nair RP, Franke A, Barker JNWN, Abecasis GR, Elder JT, Trembath RC. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat Genet 2012; 44:1341-8. [PMID: 23143594 PMCID: PMC3510312 DOI: 10.1038/ng.2467] [Citation(s) in RCA: 741] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 10/17/2012] [Indexed: 02/08/2023]
Abstract
To gain further insight into the genetic architecture of psoriasis, we conducted a meta-analysis of 3 genome-wide association studies (GWAS) and 2 independent data sets genotyped on the Immunochip, including 10,588 cases and 22,806 controls. We identified 15 new susceptibility loci, increasing to 36 the number associated with psoriasis in European individuals. We also identified, using conditional analyses, five independent signals within previously known loci. The newly identified loci shared with other autoimmune diseases include candidate genes with roles in regulating T-cell function (such as RUNX3, TAGAP and STAT3). Notably, they included candidate genes whose products are involved in innate host defense, including interferon-mediated antiviral responses (DDX58), macrophage activation (ZC3H12C) and nuclear factor (NF)-κB signaling (CARD14 and CARM1). These results portend a better understanding of shared and distinctive genetic determinants of immune-mediated inflammatory disorders and emphasize the importance of the skin in innate and acquired host defense.
Collapse
Affiliation(s)
- Lam C Tsoi
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jo Knight
- Neuroscience Research, Centre for Addiction and Mental Health, Toronto, ON, Canada M5T 1R8
- National Institute for Health Research (NIHR), Biomedical Research Centre, Guy’s and St. Thomas’ NHS Foundation Trust
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Capon
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jun Ding
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Yanming Li
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Hyun M Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Michael H Allen
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Ross McManus
- Department of Clinical Medicine Trinity College Dublin, Ireland
- Institute of Molecular Medicine, Trinity College Dublin, Ireland
| | - Giuseppe Novelli
- National Agency for Evaluation of Universities and Research Institutes (ANVUR)
- Research Center San Pietro Hospital, Rome, Italy
| | - Lena Samuelsson
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Joost Schalkwijk
- Department of Dermatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Mona Ståhle
- Dermatology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Catherine H Smith
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Michael J Cork
- Academic Unit of Dermatology Research, Department of Infection and Immunity, The University of Sheffield, Sheffield, UK
| | - Xavier Estivill
- Genes and Disease Programme, Centre for Genomic Regulation (CRG) and UPF, Hospital del Mar Research Institute (CRG) and Public Health and Epidemiology Network Biomedical Research Centre (CIBERESP), Barcelona, Spain
| | - Anne M Bowcock
- Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | | | - Wolfgang Weger
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachid Tazi-Ahnini
- Academic Unit of Dermatology Research, Department of Infection and Immunity, The University of Sheffield, Sheffield, UK
| | - Frank O Nestle
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Adrian Hayday
- Division of Immunology, Infection and Inflammatory Disease; King’s College London, London, UK
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 54127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, 54127 Bonn, Germany
| | - Juliane Winkelmann
- Department of Neurology, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Munich, Germany
| | - Cisca Wijmenga
- Genetics Department, University Medical Center and University of Groningen, Groningen, The Netherlands
| | | | - Sarah Edkins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Amy Strange
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Richard D Pearson
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Damjan Vukcevic
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Chris CA Spencer
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | | | - Ulrich Mrowietz
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
- PopGen biobank, University Hospital S.-H., Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Sulev Koks
- Department of Physiology, Centre of Translational Medicine and Centre for Translational Genomics, University of Tartu, 50409 Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology and Venerology, University of Tartu, 50409 Tartu, Estonia
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael Weichenthal
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - H. Erich Wichmann
- Institute of Epidemiology I, Helmholtz Centre Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University, 81377 Munich, Germany
- Klinikum Grosshadern, 81377 Munich, Germany
| | - Vinod Chandran
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8, Canada
| | - Cheryl F Rosen
- Department of Medicine, Division of Dermatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8
| | - Proton Rahman
- Department of Medicine, Memorial University, St. John’s, Newfoundland A1C 5B8, Canada
| | - Dafna D Gladman
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8, Canada
| | - Christopher EM Griffiths
- Dermatological Sciences, Salford Royal NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Andre Reis
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Finland
| | | | | | | | | | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Jonathan NWN Barker
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
- Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London, UK
| |
Collapse
|
233
|
Eyre S, Bowes J, Diogo D, Lee A, Barton A, Martin P, Zhernakova A, Stahl E, Viatte S, McAllister K, Amos CI, Padyukov L, Toes RE, Huizinga TW, Wijmenga C, Trynka G, Franke L, Westra HJ, Alfredsson L, Hu X, Sandor C, de Bakker PI, Davila S, Khor CC, Heng KK, Andrews R, Edkins S, Hunt SE, Langford C, Symmons D, Concannon P, Onengut-Gumuscu S, Rich SS, Deloukas P, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Ärlsetig L, Martin J, Rantapää-Dahlqvist S, Plenge R, Raychaudhuri S, Klareskog L, Gregersen PK, Worthington J. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat Genet 2012; 44:1336-40. [PMID: 23143596 PMCID: PMC3605761 DOI: 10.1038/ng.2462] [Citation(s) in RCA: 476] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 10/10/2012] [Indexed: 12/17/2022]
Abstract
Using the Immunochip custom SNP array, which was designed for dense genotyping of 186 loci identified through genome-wide association studies (GWAS), we analyzed 11,475 individuals with rheumatoid arthritis (cases) of European ancestry and 15,870 controls for 129,464 markers. We combined these data in a meta-analysis with GWAS data from additional independent cases (n = 2,363) and controls (n = 17,872). We identified 14 new susceptibility loci, 9 of which were associated with rheumatoid arthritis overall and five of which were specifically associated with disease that was positive for anticitrullinated peptide antibodies, bringing the number of confirmed rheumatoid arthritis risk loci in individuals of European ancestry to 46. We refined the peak of association to a single gene for 19 loci, identified secondary independent effects at 6 loci and identified association to low-frequency variants at 4 loci. Bioinformatic analyses generated strong hypotheses for the causal SNP at seven loci. This study illustrates the advantages of dense SNP mapping analysis to inform subsequent functional investigations.
Collapse
Affiliation(s)
- Steve Eyre
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research , University of Manchester, Manchester Academic Health Science Centre
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre
| | - John Bowes
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research , University of Manchester, Manchester Academic Health Science Centre
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre
| | - Dorothée Diogo
- Division of Rheumatology, Immunology, and Allergy Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Division of Genetics, Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
| | - Annette Lee
- The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, New York, USA
| | - Anne Barton
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research , University of Manchester, Manchester Academic Health Science Centre
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre
| | - Paul Martin
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research , University of Manchester, Manchester Academic Health Science Centre
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre
| | - Alexandra Zhernakova
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Eli Stahl
- Division of Rheumatology, Immunology, and Allergy Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Division of Genetics, Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
| | - Sebastien Viatte
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research , University of Manchester, Manchester Academic Health Science Centre
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre
| | - Kate McAllister
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research , University of Manchester, Manchester Academic Health Science Centre
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre
| | | | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Rene E.M. Toes
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tom W.J. Huizinga
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Gosia Trynka
- Division of Rheumatology, Immunology, and Allergy Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Division of Genetics, Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Lars Alfredsson
- Department of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Xinli Hu
- Division of Rheumatology, Immunology, and Allergy Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Division of Genetics, Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, Boston, Massachusetts
| | - Cynthia Sandor
- Division of Rheumatology, Immunology, and Allergy Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Division of Genetics, Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
| | - Paul I.W. de Bakker
- Division of Rheumatology, Immunology, and Allergy Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Division of Genetics, Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
- Department of Epidemiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sonia Davila
- Division of Human Genetics, Genome Institute of Singapore , Singapore
| | - Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore , Singapore
| | - Khai Koon Heng
- Division of Human Genetics, Genome Institute of Singapore , Singapore
| | | | - Sarah Edkins
- The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sarah E Hunt
- The Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - Deborah Symmons
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research , University of Manchester, Manchester Academic Health Science Centre
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre
| | | | | | - Pat Concannon
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | | | | | | | - Lisbeth Ärlsetig
- Departments of Public Health and Clinical Medicine Umeå University, Umeå, Sweden
- Rheumatology, Umeå University, Umeå, Sweden
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, Avenida del Conocimiento s/n, Granada, 18100, Spain
| | - Solbritt Rantapää-Dahlqvist
- Departments of Public Health and Clinical Medicine Umeå University, Umeå, Sweden
- Rheumatology, Umeå University, Umeå, Sweden
| | - Robert Plenge
- Division of Rheumatology, Immunology, and Allergy Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Division of Genetics, Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
| | - Soumya Raychaudhuri
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research , University of Manchester, Manchester Academic Health Science Centre
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre
- Division of Rheumatology, Immunology, and Allergy Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Division of Genetics, Brigham and Women’s, Hospital, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Peter K Gregersen
- The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, New York, USA
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, Centre for Musculoskeletal Research , University of Manchester, Manchester Academic Health Science Centre
- National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre
| |
Collapse
|
234
|
Selmi C, Lu Q, Humble MC. Heritability versus the role of the environment in autoimmunity. J Autoimmun 2012; 39:249-52. [DOI: 10.1016/j.jaut.2012.07.011] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 07/31/2012] [Indexed: 01/07/2023]
|
235
|
Johnson K, Wong R, Barriga KJ, Klingensmith G, Ziegler AG, Rewers MJ, Steck AK. rs11203203 is associated with type 1 diabetes risk in population pre-screened for high-risk HLA-DR,DQ genotypes. Pediatr Diabetes 2012; 13:611-5. [PMID: 22776074 PMCID: PMC4886718 DOI: 10.1111/j.1399-5448.2012.00888.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/08/2012] [Accepted: 05/15/2012] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE To evaluate UBASH3A (rs11203203) as a predictor of persistent islet autoimmunity (IA) and type 1 diabetes (T1D). RESEARCH DESIGN AND METHODS The Diabetes Autoimmunity Study in the Young (DAISY) followed prospectively for development of persistent IA (autoantibodies to insulin, GAD65, IA-2, or ZnT8 on at least two consecutive exams) and diabetes 1715 non-Hispanic white children at increased genetic risk for T1D. The DAISY participants were genotyped for rs11202203 (UBASH3A). RESULTS UBASH3A allele A was associated with development of IA [hazard ratio (HR) = 1.46, 95%CI = 1.11-1.91, p = 0.007] and diabetes (HR = 1.84, 95%CI = 1.28-2.64, p = 0.001), controlling for presence of HLA-DR3/4,DQB1*0302 and having a first-degree relative (FDR) with T1D. The UBASH3A AA genotype conferred higher risk of persistent IA (12.7%) and diabetes (6.1%) by age 10 than for AG (7.7 and 3.1%, respectively) or GG (5.3 and 2.0%) genotype (p = 0.009 for IA, p = 0.0004 for diabetes). Among children with no family history of T1D, but HLA-DR3/4,DQB1*0302 and UBASH3A AA genotype, 35.9% developed IA and 50.6% developed diabetes by age 15. CONCLUSIONS UBASH3A appears to be an independent predictor of IA and T1D in children, including those free of family history of T1D but carrying the HLA-DR3/4,DQB1*0302 genotype. If confirmed, UBASH3A may prove useful in T1D risk prediction and pre-screening of the general population children for clinical trials.
Collapse
Affiliation(s)
- Kelly Johnson
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver (UCD), Mail Stop A140, 1775 Aurora Ct, Aurora, CO 80045, USA
| | - Randall Wong
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver (UCD), Mail Stop A140, 1775 Aurora Ct, Aurora, CO 80045, USA
| | - Katherine J. Barriga
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver (UCD), Mail Stop A140, 1775 Aurora Ct, Aurora, CO 80045, USA
| | - Georgeanna Klingensmith
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver (UCD), Mail Stop A140, 1775 Aurora Ct, Aurora, CO 80045, USA
| | - Anette-G Ziegler
- Diabetes Research Institute, Forschergruppe Diabetes e.V. at Helmholtz Zentrum, Technische Universitat, Munich, Germany
| | - Marian J. Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver (UCD), Mail Stop A140, 1775 Aurora Ct, Aurora, CO 80045, USA
| | - Andrea K. Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver (UCD), Mail Stop A140, 1775 Aurora Ct, Aurora, CO 80045, USA
| |
Collapse
|
236
|
TNFAIP3 gene polymorphisms confer risk for Behcet’s disease in a Chinese Han population. Hum Genet 2012; 132:293-300. [DOI: 10.1007/s00439-012-1250-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/05/2012] [Indexed: 01/01/2023]
|
237
|
Alcina A, Fedetz M, Fernández O, Saiz A, Izquierdo G, Lucas M, Leyva L, García-León JA, Abad-Grau MDM, Alloza I, Antigüedad A, Garcia-Barcina MJ, Vandenbroeck K, Varadé J, de la Hera B, Arroyo R, Comabella M, Montalban X, Petit-Marty N, Navarro A, Otaegui D, Olascoaga J, Blanco Y, Urcelay E, Matesanz F. Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis. J Med Genet 2012; 50:25-33. [PMID: 23160276 PMCID: PMC3538279 DOI: 10.1136/jmedgenet-2012-101085] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background and aim Several studies have highlighted the association of the 12q13.3–12q14.1 region with coeliac disease, type 1 diabetes, rheumatoid arthritis and multiple sclerosis (MS); however, the causal variants underlying diseases are still unclear. The authors sought to identify the functional variant of this region associated with MS. Methods Tag-single nucleotide polymorphism (SNP) analysis of the associated region encoding 15 genes was performed in 2876 MS patients and 2910 healthy Caucasian controls together with expression regulation analyses. Results rs6581155, which tagged 18 variants within a region where 9 genes map, was sufficient to model the association. This SNP was in total linkage disequilibrium (LD) with other polymorphisms that associated with the expression levels of FAM119B, AVIL, TSFM, TSPAN31 and CYP27B1 genes in different expression quantitative trait loci studies. Functional annotations from Encyclopedia of DNA Elements (ENCODE) showed that six out of these rs6581155-tagged-SNPs were located in regions with regulatory potential and only one of them, rs10877013, exhibited allele-dependent (ratio A/G=9.5-fold) and orientation-dependent (forward/reverse=2.7-fold) enhancer activity as determined by luciferase reporter assays. This enhancer is located in a region where a long-range chromatin interaction among the promoters and promoter-enhancer of several genes has been described, possibly affecting their expression simultaneously. Conclusions This study determines a functional variant which alters the enhancer activity of a regulatory element in the locus affecting the expression of several genes and explains the association of the 12q13.3–12q14.1 region with MS.
Collapse
Affiliation(s)
- Antonio Alcina
- Department of Cell Biology and Immunology Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas (IPBLNCSIC), Granada, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
238
|
Stanford SM, Rapini N, Bottini N. Regulation of TCR signalling by tyrosine phosphatases: from immune homeostasis to autoimmunity. Immunology 2012; 137:1-19. [PMID: 22862552 DOI: 10.1111/j.1365-2567.2012.03591.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
More than half of the known protein tyrosine phosphatases (PTPs) in the human genome are expressed in T cells, and significant progress has been made in elucidating the biology of these enzymes in T-cell development and function. Here we provide a systematic review of the current understanding of the roles of PTPs in T-cell activation, providing insight into their mechanisms of action and regulation in T-cell receptor signalling, the phenotypes of their genetically modified mice, and their possible involvement in T-cell-mediated autoimmune disease. Our projection is that the interest in PTPs as mediators of T-cell homeostasis will continue to rise with further functional analysis of these proteins, and PTPs will be increasingly considered as targets of immunomodulatory therapies.
Collapse
Affiliation(s)
- Stephanie M Stanford
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | | |
Collapse
|
239
|
Chatzikyriakidou A, Voulgari PV, Georgiou I, Drosos AA. Altered sequence of the ETS1 transcription factor may predispose to rheumatoid arthritis susceptibility. Scand J Rheumatol 2012; 42:11-4. [PMID: 23101665 DOI: 10.3109/03009742.2012.711367] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE ETS1 belongs to the ETS family of transcription factors that regulate the expression of various immune-related genes. The aim of this study was to identify whether the ETS1 single nucleotide polymorphism (SNP) rs11221332, described in Caucasian subjects, plays a role in rheumatoid arthritis (RA) susceptibility. METHODS We genotyped this polymorphism in 136 unrelated patients with RA and 147 healthy individuals with no history of autoimmune disease. Genotyping was performed with a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay and the data were analysed using SPSS statistical software. RESULTS A statistically significant difference was observed in the distribution of the rs11221332 genotypes between RA patients and controls (p = 0.041). Comparing the distribution of rs11221332 alleles between the groups studied, a greater difference was found [odds ratio (OR) 1.504, 95% confidence interval (CI) 1.036-2.183; p = 0.039]. CONCLUSIONS The present study revealed, for first time, the positive association of a polymorphism in the sequence of the ETS1 transcription factor with RA susceptibility. Further studies in other ethnic groups of patients are needed to confirm the results of the present genetic association study related to ETS1, a widely used transcription factor in the regulation of the expression of various genes.
Collapse
Affiliation(s)
- A Chatzikyriakidou
- Department of Obstetrics and Gynaecology, Medical School, University of Ioannina, Ioannina, Greece
| | | | | | | |
Collapse
|
240
|
Do R, Kathiresan S, Abecasis GR. Exome sequencing and complex disease: practical aspects of rare variant association studies. Hum Mol Genet 2012; 21:R1-9. [PMID: 22983955 PMCID: PMC3459641 DOI: 10.1093/hmg/dds387] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 09/07/2012] [Indexed: 11/13/2022] Open
Abstract
Genetic association and linkage studies can provide insights into complex disease biology, guiding the development of new diagnostic and therapeutic strategies. Over the past decade, genetic association studies have largely focused on common, easy to measure genetic variants shared between many individuals. These common variants typically have subtle functional consequence and translating the resulting association signals into biological insights can be challenging. In the last few years, exome sequencing has emerged as a cost-effective strategy for extending these studies to include rare coding variants, which often have more marked functional consequences. Here, we provide practical guidance in the design and analysis of complex trait association studies focused on rare, coding variants.
Collapse
Affiliation(s)
- Ron Do
- Center for Human Genetic Research and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA and
| | - Sekar Kathiresan
- Center for Human Genetic Research and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA and
| | - Gonçalo R. Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| |
Collapse
|
241
|
Voight BF, Cotsapas C. Human genetics offers an emerging picture of common pathways and mechanisms in autoimmunity. Curr Opin Immunol 2012; 24:552-7. [PMID: 23041452 DOI: 10.1016/j.coi.2012.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 06/22/2012] [Accepted: 07/01/2012] [Indexed: 12/29/2022]
Abstract
In genetic studies of autoimmune and inflammatory diseases, one clear finding that has emerged from genome-wide association studies is that a substantial fraction of variation modifying risk in one disease also contributes mediate risk to multiple, additional autoimmune and inflammatory diseases. The unexpected magnitude of this overlap presents the unique opportunity to dissect the pathogenic mechanisms underlying multiple disease states in the expectation that this may lead to both more sensitive diagnostics and novel therapies. Here, we review the current evidence for this shared genetic architecture and, based on these data, outline models for shared pathways, the underlying hypotheses for them, how these models can be tested and validated.
Collapse
Affiliation(s)
- Benjamin F Voight
- Departments of Pharmacology and Genetics, The University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, United States.
| | | |
Collapse
|
242
|
|
243
|
Maiti AK, Nath SK. Gene network analysis of small molecules with autoimmune disease associated genes predicts a novel strategy for drug efficacy. Autoimmun Rev 2012; 12:510-22. [PMID: 23000205 DOI: 10.1016/j.autrev.2012.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 09/10/2012] [Indexed: 02/09/2023]
Abstract
Numerous genes/SNPs in autoimmune diseases (ADs) are identified through genome-wide association studies (GWAS) and likely to contribute in developing autoimmune phenotypes. Constructions of biologically meaningful pathways are necessary to determine how these genes interact with each other and with other small molecules to develop various complex AD phenotypes prior to beginning time-consuming rigorous experimentation. We have constructed biological pathways with genetically identified genes leading to shared AD phenotypes. Various environmental and endogenous factors interact with these AD associated genes suggesting their critical role in developing diseases and further association studies could be designed for assessing the role of these factors with risk allele in a specific gene. Additionally, existing drugs that have been used long before the identification of these genetically associated genes also interact with these newly associated genes. Thus advanced therapeutic strategies could be designed by grouping patients with risk allele(s) in particular genes that directly or closely interact with the specified drugs. This drug-susceptible gene network will not only increase our understanding about the additional molecular basis for effectiveness against these diseases but also indicate which drug could be more effective for those patients carrying risk allele(s) in that gene. Additionally, we have also identified several interlinking genes in the pathways that could be used for designing future association studies.
Collapse
Affiliation(s)
- Amit K Maiti
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104, United States.
| | | |
Collapse
|
244
|
Abstract
Autoimmunity and allergy involving the digestive system may be considered as paradigmatic for numerous common themes of complex diseases secondary to tolerance breakdown. Among gastrointestinal autoimmune diseases, for example, we encounter diseases in which a clear environmental trigger is identified (i.e., celiac disease), serum autoantibodies are most specific (i.e., primary biliary cirrhosis), or in which the disease pathophysiology is clearly understood (i.e., autoimmune gastritis). Similarly, it is intriguing that the gastrointestinal tract and the liver circulation represent the crucial environment for the development of immune tolerance. This issue is dedicated to the discussion of recent concepts while identifying two major common issues, i.e., the need for serum biomarkers and the role of vitamin D. Other common themes characterize the etiology and effector mechanisms of these and other autoimmune diseases and are discussed in each cutting-edge overview.
Collapse
|
245
|
Hartley SW, Monti S, Liu CT, Steinberg MH, Sebastiani P. Bayesian methods for multivariate modeling of pleiotropic SNP associations and genetic risk prediction. Front Genet 2012; 3:176. [PMID: 22973300 PMCID: PMC3438684 DOI: 10.3389/fgene.2012.00176] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/20/2012] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified numerous associations between genetic loci and individual phenotypes; however, relatively few GWAS have attempted to detect pleiotropic associations, in which loci are simultaneously associated with multiple distinct phenotypes. We show that pleiotropic associations can be directly modeled via the construction of simple Bayesian networks, and that these models can be applied to produce single or ensembles of Bayesian classifiers that leverage pleiotropy to improve genetic risk prediction. The proposed method includes two phases: (1) Bayesian model comparison, to identify Single-Nucleotide Polymorphisms (SNPs) associated with one or more traits; and (2) cross-validation feature selection, in which a final set of SNPs is selected to optimize prediction. To demonstrate the capabilities and limitations of the method, a total of 1600 case-control GWAS datasets with two dichotomous phenotypes were simulated under 16 scenarios, varying the association strengths of causal SNPs, the size of the discovery sets, the balance between cases and controls, and the number of pleiotropic causal SNPs. Across the 16 scenarios, prediction accuracy varied from 90 to 50%. In the 14 scenarios that included pleiotropically associated SNPs, the pleiotropic model search and prediction methods consistently outperformed the naive model search and prediction. In the two scenarios in which there were no true pleiotropic SNPs, the differences between the pleiotropic and naive model searches were minimal. To further evaluate the method on real data, a discovery set of 1071 sickle cell disease (SCD) patients was used to search for pleiotropic associations between cerebral vascular accidents and fetal hemoglobin level. Classification was performed on a smaller validation set of 352 SCD patients, and showed that the inclusion of pleiotropic SNPs may slightly improve prediction, although the difference was not statistically significant. The proposed method is robust, computationally efficient, and provides a powerful new approach for detecting and modeling pleiotropic disease loci.
Collapse
Affiliation(s)
- Stephen W Hartley
- Department of Biostatistics, Boston University School of Public Health Boston, MA, USA
| | | | | | | | | |
Collapse
|
246
|
Association analyses identify three susceptibility Loci for vitiligo in the Chinese Han population. J Invest Dermatol 2012; 133:403-10. [PMID: 22951725 DOI: 10.1038/jid.2012.320] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To identify susceptibility loci for vitiligo, we extended our previous vitiligo genome-wide association study with a two-staged replication study that included 6,857 cases and 12,025 controls from the Chinese Han population. We identified three susceptibility loci, 12q13.2 (rs10876864, P(combined)=8.07 × 10(-12), odds ratio (OR)=1.18), 11q23.3 (rs638893, P(combined)=2.47 × 10(-9), OR=1.22), and 10q22.1 (rs1417210, P(combined)=1.83 × 10(-8), OR=0.88), and confirmed three previously reported loci for vitiligo, 3q28 (rs9851967, P(combined)=8.57 × 10(-8), OR=0.88), 10p15.1 (rs3134883, P(combined)=1.01 × 10(-5), OR=1.11), and 22q12.3 (rs2051582, P(combined)=2.12 × 10(-5), OR=1.14), in the Chinese Han population. The most significant single-nucleotide polymorphism in the 12q13.2 locus is located immediately upstream of the promoter region of PMEL, which encodes a major melanocyte antigen and has expression loss in the vitiligo lesional skin. In addition, both 12q13.2 and 11q23.3 loci identified in this study are also associated with other autoimmune diseases such as type 1 diabetes and systemic lupus erythematosus. These findings provide indirect support that vitiligo pathogenesis involves a complex interplay between immune regulatory factors and melanocyte-specific factors. They also highlight similarities and differences in the genetic basis of vitiligo in Chinese and Caucasian populations.
Collapse
|
247
|
Wang S, Adrianto I, Wiley GB, Lessard CJ, Kelly JA, Adler AJ, Glenn SB, Williams AH, Ziegler JT, Comeau ME, Marion MC, Wakeland BE, Liang C, Kaufman KM, Guthridge JM, Alarcón-Riquelme ME, Alarcón GS, Anaya JM, Bae SC, Kim JH, Joo YB, Boackle SA, Brown EE, Petri MA, Ramsey-Goldman R, Reveille JD, Vilá LM, Criswell LA, Edberg JC, Freedman BI, Gilkeson GS, Jacob CO, James JA, Kamen DL, Kimberly RP, Martin J, Merrill JT, Niewold TB, Pons-Estel BA, Scofield RH, Stevens AM, Tsao BP, Vyse TJ, Langefeld CD, Harley JB, Wakeland EK, Moser KL, Montgomery CG, Gaffney PM. A functional haplotype of UBE2L3 confers risk for systemic lupus erythematosus. Genes Immun 2012; 13:380-7. [PMID: 22476155 PMCID: PMC3411915 DOI: 10.1038/gene.2012.6] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 02/29/2012] [Accepted: 03/06/2012] [Indexed: 02/07/2023]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with diverse clinical manifestations characterized by the development of pathogenic autoantibodies manifesting in inflammation of target organs such as the kidneys, skin and joints. Genome-wide association studies have identified genetic variants in the UBE2L3 region that are associated with SLE in subjects of European and Asian ancestry. UBE2L3 encodes an ubiquitin-conjugating enzyme, UBCH7, involved in cell proliferation and immune function. In this study, we sought to further characterize the genetic association in the region of UBE2L3 and use molecular methods to determine the functional effect of the risk haplotype. We identified significant associations between variants in the region of UBE2L3 and SLE in individuals of European and Asian ancestry that exceeded a Bonferroni-corrected threshold (P<1 × 10(-4)). A single risk haplotype was observed in all associated populations. Individuals harboring the risk haplotype display a significant increase in both UBE2L3 mRNA expression (P=0.0004) and UBCH7 protein expression (P=0.0068). The results suggest that variants carried on the SLE-associated UBE2L3 risk haplotype influence autoimmunity by modulating UBCH7 expression.
Collapse
Affiliation(s)
- Shaofeng Wang
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Indra Adrianto
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Graham B. Wiley
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Christopher J. Lessard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Adam J. Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Stuart B. Glenn
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Adrienne H. Williams
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Julie T. Ziegler
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Mary E. Comeau
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Miranda C. Marion
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Benjamin E. Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Chaoying Liang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Kenneth M. Kaufman
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- US Department of Veterans Affairs Medical Center, Cincinnati, OH
| | - Joel M. Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Marta E. Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
- Centro de Genómica e Investigaciones Oncológicas (GENyO), Pfizer-Universidad de Granada-Junta de Andalucía Granada, Spain
| | | | | | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea
| | - Jae-Hoon Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea
| | - Young Bin Joo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea
| | - Susan A. Boackle
- Division of Rheumatology, University of Colorado Denver, Aurora, CO
| | - Elizabeth E. Brown
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL
| | - Michelle A. Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - John D. Reveille
- Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, TX
| | - Luis M. Vilá
- Department of Medicine, Division of Rheumatology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Lindsey A. Criswell
- Rosalind Russell Medical Research Center for Arthritis, University of California San Francisco, San Francisco, CA
| | - Jeffrey C. Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Barry I. Freedman
- Department of Internal Medicine/Nephrology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Gary S. Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC
| | - Chaim O. Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA
| | - Judith A. James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Diane L. Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC
| | - Robert P. Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Javier Martin
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Joan T. Merrill
- Clinical Pharmacology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Timothy B. Niewold
- Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL
| | | | - R. Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Anne M. Stevens
- Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, WA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
| | - Betty P. Tsao
- Division of Rheumatology, Department of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Timothy J. Vyse
- Divisions of Genetics and Molecular Medicine and Immunology, Infection and Inflammatory Diseases, King’s College London, London, UK
| | - Carl D. Langefeld
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - John B. Harley
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- US Department of Veterans Affairs Medical Center, Cincinnati, OH
| | - Edward K. Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Kathy L. Moser
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Courtney G. Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| |
Collapse
|
248
|
Harris CL, Heurich M, Rodriguez de Cordoba S, Morgan BP. The complotype: dictating risk for inflammation and infection. Trends Immunol 2012; 33:513-21. [PMID: 22749446 PMCID: PMC3460238 DOI: 10.1016/j.it.2012.06.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 06/02/2012] [Accepted: 06/04/2012] [Indexed: 12/19/2022]
Abstract
Complement is a key component of immune defence against infection; it potently drives inflammation at sites of pathology and is essential for killing of pathogens. Genetic linkage of common complement polymorphisms to disease has advanced the concept that subtle changes in complement activity significantly affect disease risk. Functional analyses of disease-linked polymorphic variants demonstrate that, although individual polymorphisms cause only small changes in activity, when combined, the aggregate effects are large. The inherited set of common variants, the complotype, thus has a major impact on susceptibility to inflammatory and infectious diseases. Assessing the complotype of an individual will aid prediction of disease risk and inform intervention to reduce or eliminate risk.
Collapse
Affiliation(s)
- Claire L Harris
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | | | | | | |
Collapse
|
249
|
O'Shea JJ, Plenge R. JAK and STAT signaling molecules in immunoregulation and immune-mediated disease. Immunity 2012; 36:542-50. [PMID: 22520847 DOI: 10.1016/j.immuni.2012.03.014] [Citation(s) in RCA: 826] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Indexed: 12/12/2022]
Abstract
The discovery of the Janus kinase (JAK)-signal transducer and activator of transcripton (STAT) signaling pathway, a landmark in cell biology, provided a simple mechanism for gene regulation that dramatically advanced our understanding of the action of hormones, interferons, colony-stimulating factors, and interleukins. As we learn more about the complexities of immune responses, new insights into the functions of this pathway continue to be revealed, aided by technology that permits genome-wide views. As we celebrate the 20(th) anniversary of the discovery of this paradigm in cell signaling, it is particularly edifying to see how this knowledge has rapidly been translated to human immune disease. Not only have genome-wide association studies demonstrated that this pathway is highly relevant to human autoimmunity, but targeting JAKs is now a reality in immune-mediated disease.
Collapse
Affiliation(s)
- John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | | |
Collapse
|
250
|
Parmar AS, Lappalainen M, Paavola-Sakki P, Halme L, Färkkilä M, Turunen U, Kontula K, Aromaa A, Salomaa V, Peltonen L, Halfvarson J, Törkvist L, D'Amato M, Saavalainen P, Einarsdottir E. Association of celiac disease genes with inflammatory bowel disease in Finnish and Swedish patients. Genes Immun 2012; 13:474-80. [DOI: 10.1038/gene.2012.21] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|