1
|
Yang Z, Wang C, Erjavec S, Petukhova L, Christiano A, Ionita-Laza I. A semi-supervised model to predict regulatory effects of genetic variants at single nucleotide resolution using massively parallel reporter assays. Bioinformatics 2021; 37:btab040. [PMID: 33515242 PMCID: PMC8337004 DOI: 10.1093/bioinformatics/btab040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/28/2022] Open
Abstract
MOTIVATION Predicting regulatory effects of genetic variants is a challenging but important problem in functional genomics. Given the relatively low sensitivity of functional assays, and the pervasiveness of class imbalance in functional genomic data, popular statistical prediction models can sharply underestimate the probability of a regulatory effect. We describe here the presence-only model (PO-EN), a type of semi-supervised model, to predict regulatory effects of genetic variants at sequence-level resolution in a context of interest by integrating a large number of epigenetic features and massively parallel reporter assays (MPRAs). RESULTS Using experimental data from a variety of MPRAs we show that the presence-only model produces better calibrated predicted probabilities and has increased accuracy relative to state-of-the-art prediction models. Furthermore, we show that the predictions based on pre-trained PO-EN models are useful for prioritizing functional variants among candidate eQTLs and significant SNPs at GWAS loci. In particular, for the costimulatory locus, associated with multiple autoimmune diseases, we show evidence of a regulatory variant residing in an enhancer 24.4 kb downstream of CTLA4, with evidence from capture Hi-C of interaction with CTLA4. Furthermore, the risk allele of the regulatory variant is on the same risk increasing haplotype as a functional coding variant in exon 1 of CTLA4, suggesting that the regulatory variant acts jointly with the coding variant leading to increased risk to disease. AVAILABILITY The presence-only model is implemented in the R package 'PO.EN', freely available on CRAN. A vignette describing a detailed demonstration of using the proposed PO-EN model can be found on github at https://github.com/Iuliana-Ionita-Laza/PO.EN/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Zikun Yang
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Chen Wang
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Stephanie Erjavec
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Lynn Petukhova
- Department of Epidemiology, Columbia University, New York, NY 10032, USA
- Department of Dermatology, Columbia University, New York, NY 10032, USA
| | - Angela Christiano
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA
- Department of Dermatology, Columbia University, New York, NY 10032, USA
| | | |
Collapse
|
2
|
Hu J, Li QL, Hou SH, Peng H, Guo JJ. Association of Inducible T Cell Costimulator Polymorphisms with Susceptibility and Outcome of Hepatitis B Virus Infection in a Chinese Han Population. Scand J Immunol 2015; 82:275-81. [PMID: 26074057 DOI: 10.1111/sji.12319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 05/21/2015] [Indexed: 12/13/2022]
Abstract
Inducible T cell costimulator (ICOS) functions to regulate cell-cell signalling, immune responses and cell proliferation. ICOS single nucleotide polymorphism (SNP) may affect protein expression and functions. This study investigated the association of ICOS SNPs with hepatitis B virus (HBV) infection and outcome in a Chinese population. A total of 1290 Chinese Han individuals were enrolled, including 63 asymptomatic HBV carriers, 220 chronic hepatitis B patients (CHB), 249 HBV-related liver cirrhosis patients (LC), 108 patients with HBV-related hepatocellular carcinoma (HCC), 338 patients with natural HBV clearance and 312 healthy subjects (as controls). DNA samples from these subjects were genotyped for four ICOS SNPs (rs11883722, rs10932029, rs1559931 and rs4675379) using TaqMan SNP Genotyping Assay and analysed. The data showed that genotype and allele frequencies of ICOS SNPs in cases and controls followed the Hardy-Weinberg distribution. The CC genotype of rs4675379 was higher in patients with HBV infection (including AC, CHB, LC and HCC) than in patients with HBV clearance (P = 0.006). Furthermore, the genotype 'GA' and the minor allele 'A' of rs1559931 were associated with a decreased HCC susceptibility (P < 0.001). Haplotype analysis data showed that 'GC' haplotype in block 2 (rs1559931 and rs4675379) had a lower frequency in patients than in HBV-cleared subjects (P = 0.034), although its overall frequency was only 1.6%. Our study found that ICOS rs1559931 SNP was associated with decreased HBV-related HCC risk in the studied Chinese Han population, except for patients with natural clearance of HBV.
Collapse
Affiliation(s)
- J Hu
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Q-L Li
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - S-H Hou
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - H Peng
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - J-J Guo
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
3
|
Song GG, Kim JH, Kim YH, Lee YH. Association between CTLA-4 polymorphisms and susceptibility to Celiac disease: A meta-analysis. Hum Immunol 2013; 74:1214-8. [DOI: 10.1016/j.humimm.2013.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 04/12/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
|
4
|
Romanos J, Rybak A, Wijmenga C, Wapenaar MC. Molecular diagnosis of celiac disease: are we there yet? ACTA ACUST UNITED AC 2013; 2:399-416. [PMID: 23495707 DOI: 10.1517/17530059.2.4.399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Celiac disease (CD) is a complex genetic disorder of the small intestine resulting from aberrant cellular responses to gluten peptides. It may affect as much as 1% of the Western population and the only treatment is a lifelong gluten-free diet. Allelic variants of the HLA-DQ locus, coding for the HLA-DQ2 and HLA-DQ8 molecules, contribute to ∼ 40% of CD etiology, whereas other genes, such as MYO9B, CTLA4, IL2, IL21, PARD3 and MAGI2, have only a modest effect. Most of these genes have shown varied association among different populations and an overlap with other autoimmune or inflammatory disorders, indicating that such disorders may share common pathways. OBJECTIVES In this review, a molecular approach into diagnostics of celiac disease is shown. CONCLUSIONS Genome-wide association studies will allow more genes to be identified, and knowing how risk variants combine will help to predict better the risk for the individual. HLA typing can already be used to identify high-risk individuals.
Collapse
Affiliation(s)
- Jihane Romanos
- PhD student University of Groningen, University Medical Center Groningen, Department of Genetics, PO Box 30001, 9700 RB Groningen, The Netherlands
| | | | | | | |
Collapse
|
5
|
Association of genetic variation in co-stimulatory molecule genes with outcome of liver transplant in Iranian patients. Gene 2012; 504:127-32. [DOI: 10.1016/j.gene.2012.04.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 03/01/2012] [Accepted: 04/18/2012] [Indexed: 01/10/2023]
|
6
|
Brophy K, Ryan AW, Turner G, Trimble V, Patel KD, O'Morain C, Kennedy NP, Egan B, Close E, Lawlor G, MacMathuna P, Stevens FM, Abuzakouk M, Feighery C, Kelleher D, McManus R. Evaluation of 6 candidate genes on chromosome 11q23 for coeliac disease susceptibility: a case control study. BMC MEDICAL GENETICS 2010; 11:76. [PMID: 20478055 PMCID: PMC2880976 DOI: 10.1186/1471-2350-11-76] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 05/17/2010] [Indexed: 11/14/2022]
Abstract
Background Recent whole genome analysis and follow-up studies have identified many new risk variants for coeliac disease (CD, gluten intolerance). The majority of newly associated regions encode candidate genes with a clear functional role in T-cell regulation. Furthermore, the newly discovered risk loci, together with the well established HLA locus, account for less than 50% of the heritability of CD, suggesting that numerous additional loci remain undiscovered. Linkage studies have identified some well-replicated risk regions, most notably chromosome 5q31 and 11q23. Methods We have evaluated six candidate genes in one of these regions (11q23), namely CD3E, CD3D, CD3G, IL10RA, THY1 and IL18, as risk factors for CD using a 2-phase candidate gene approach directed at chromosome 11q. 377 CD cases and 349 ethnically matched controls were used in the initial screening, followed by an extended sample of 171 additional coeliac cases and 536 additional controls. Results Promotor SNPs (-607, -137) in the IL18 gene, which has shown association with several autoimmune diseases, initially suggested association with CD (P < 0.05). Follow-up analyses of an extended sample supported the same, moderate effect (P < 0.05) for one of these. Haplotype analysis of IL18-137/-607 also supported this effect, primarily due to one relatively rare haplotype IL18-607C/-137C (P < 0.0001), which was independently associated in two case-control comparisons. This same haplotype has been noted in rheumatoid arthritis. Conclusion Haplotypes of the IL18 promotor region may contribute to CD risk, consistent with this cytokine's role in maintaining inflammation in active CD.
Collapse
Affiliation(s)
- Karen Brophy
- Department of Clinical Medicine, Trinity Centre for Health Sciences, Trinity College Dublin, St James's Hospital, Dublin, Ireland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
CTLA4 -1661A/G and 3'UTR long repeat polymorphisms are associated with ulcerative colitis and influence CTLA4 mRNA and protein expression. Genes Immun 2010; 11:573-83. [PMID: 20445568 DOI: 10.1038/gene.2010.16] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Reduced cytotoxic T-lymphocyte antigen 4 (CTLA4) expression has been proposed as a risk for autoimmunity. CTLA4 polymorphisms have been associated with several autoimmune diseases, including ulcerative colitis (UC). In this study, we performed genotyping for CTLA4 -1661A/G, -1722T/C and 3' untranslated region (AT)n repeat polymorphisms in 300 Chinese UC patients and in 700 healthy controls, and evaluated the effects of polymorphisms on full-length (flCTLA4) and soluble CTLA4 (sCTLA4) expression in UC patients. The frequency of the -1661G allele was higher in UC patients than in healthy controls (16.5 vs 11.4%, P=0.003, odds ratio (OR)=1.53, 95% confidence interval (95% CI): 1.17-2.01). The prevalence of (AT)n repeats of the CTLA4 gene carrying long alleles (≥116 bp) was more common in UC patients than in healthy controls (22.0 vs 6.3%, P<0.001, OR=4.21, 95% CI: 2.79-6.33), and was associated with extensive colitis (P=0.008). Among UC patients, long-allele carriers expressed lower levels of flCTLA4 and sCTLA4 mRNA and sCTLA4 protein than did short-allele carriers (P<0.001, P<0.001, P<0.001, respectively). CTLA4 gene -1661A/G and long 3' untranslated region (AT)n repeat polymorphisms are associated with UC in Central China. This is likely from decreased expressions of sCTLA4 mRNA and sCTLA4 protein. Our study suggests that CTLA4 has an important role in susceptibility for UC in Central China.
Collapse
|
8
|
Simone R, Brizzolara R, Chiappori A, Milintenda-Floriani F, Natale C, Greco L, Schiavo M, Bagnasco M, Pesce G, Saverino D. A functional soluble form of CTLA-4 is present in the serum of celiac patients and correlates with mucosal injury. Int Immunol 2009; 21:1037-45. [DOI: 10.1093/intimm/dxp069] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
9
|
Yong PFK, Salzer U, Grimbacher B. The role of costimulation in antibody deficiencies: ICOS and common variable immunodeficiency. Immunol Rev 2009; 229:101-13. [PMID: 19426217 DOI: 10.1111/j.1600-065x.2009.00764.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
SUMMARY The identification of mutations in the inducible costimulator (ICOS) gene in nine patients with common variable immunodeficiency (CVID) was a major breakthrough. CVID is a complex, highly heterogeneous primary immunodeficiency disease, and the discovery of these mutations revealed a molecular basis. ICOS belongs to the CD28 family of costimulatory molecules and is expressed exclusively on activated T cells. It has at least three critical functions: germinal center formation, isotype class switching, and the development of memory B cells. The discovery of human ICOS deficiency showed that a monogenic disorder could account for the full spectrum of manifestations seen in childhood and adulthood-onset CVID, including autoimmune, inflammatory, and malignant disease complications, as well as recurrent infections. Moreover, this discovery showed that a disorder which had previously been perceived as a B-cell disease might in fact have its genetic origin in human T cells. In this article, we review the role of ICOS in the mammalian immune system and human disease, as well as the discovery and characteristics of patients with ICOS deficiency. Finally, we also discuss how these 'human knockouts' have contributed to our understanding of ICOS functions and have suggested potential avenues for using therapeutic ICOS manipulation to treat other diseases.
Collapse
Affiliation(s)
- Patrick F K Yong
- Department of Clinical Immunology, Kings College Hospital, London, UK
| | | | | |
Collapse
|
10
|
Luo Y, Xia B, Li C, Chen Z, Ge L, Jiang T, Zhou F, Zhao Y. Cytotoxic T lymphocyte antigen-4 promoter -658CT gene polymorphism is associated with ulcerative colitis in Chinese patients. Int J Colorectal Dis 2009; 24:489-93. [PMID: 19089435 DOI: 10.1007/s00384-008-0626-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2008] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIM Cytotoxic T lymphocyte antigen-4 (CTLA-4) plays a role in the downregulation of T cell activation. The present study aimed to examine an association between the CTLA-4 gene polymorphisms and ulcerative colitis (UC) in the Han Chinese in central China. MATERIALS AND METHODS One hundred seventeen patients with UC and 246 healthy controls were genotyped for CTLA-4 gene -658CT in the promoter and CT61 at the 3' untranslated region using a method of polymerase chain reaction-based restriction fragment length polymorphism and single-strand conformation polymorphism, respectively. The distributions of the genotypes and the allele frequencies of the CTLA-4 gene in UC patients and healthy controls were compared by chi-square test. RESULTS The frequency of the T/T+C/T genotype at the CTLA-4 gene -658CT in the promoter was significantly higher in UC patients than in healthy controls (26.5% vs 15.4%, chi (2) = 6.287, P = 0.015, OR = 1.973, 95%CI = 1.153-3.375). The frequency of the T allele at the CTLA-4 -658CT was also significantly higher in UC patients than in the controls (13.2% vs 8.1%, chi (2) = 4.707, P = 0.033, OR = 1.726, 95%CI = 1.049-2.838). The frequency of the T/T genotype at the -658 locus was highly associated with extensive colitis in UC patients (P = 0.037, OR = 3.955, 95%CI = 1.068-14.647). The frequency of the T allele at the -658 locus was highly associated with extensive colitis in UC patients (P = 0.0067, OR = 3.05, 95%CI = 1.320-7.048). CONCLUSION The T allele of CTLA-4 -658 polymorphism in the promoter of CTLA-4 gene was highly associated with UC in the Han Chinese in central China.
Collapse
Affiliation(s)
- Yan Luo
- Key Laboratory of Allergy and Immune-Related Diseases, School of Medicine, Wuhan University, Wuhan, Hubei Province, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Association of genetic variation in inducible costimulator gene with outcome of kidney transplantation. Transplantation 2009; 87:393-6. [PMID: 19202444 DOI: 10.1097/tp.0b013e318192897a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The closely-linked genes of CD28, cytotoxic T-lymphocyte associated antigen 4 (CTLA4), inducible costimulator (ICOS), and programmed cell death 1 on chromosome 2q encode costimulatory molecules, which are regulators of the T-cell activity. The T-cell mediated immune response has a major role in allograft rejection. Hence, the variation in these genes may have an effect on graft survival and the amount of immunosuppression needed, but so far the studies have restricted solely to the CTLA4 gene. METHODS We determined 13 single nucleotide polymorphisms in CD28, CTLA4, ICOS, and PPCD1 genes in 678 adult patients who received a kidney from deceased donor. The effect of genetic variation on the outcome of renal transplantation was analyzed. RESULTS Two markers on the ICOS gene, rs10183087 and rs4404254, were associated with delayed graft function (odds ratio=5.8; P=0.020 and odds ratio=5.8; P=0.019, respectively). Interestingly, the same ICOS variation has been shown to regulate the expression level of ICOS. We also demonstrated an association of the ICOS polymorphism rs10932037 with the graft survival (P=0.026). CONCLUSIONS The present results indicate that potentially functional genetic variation in T-cell costimulatory molecule ICOS has an effect on the outcome of kidney transplantation.
Collapse
|
12
|
Vidal C, Borg J, Xuereb-Anastasi A, Scerri CA. Variants within protectin (CD59) and CD44 genes linked to an inherited haplotype in a family with coeliac disease. TISSUE ANTIGENS 2009; 73:225-235. [PMID: 19254252 DOI: 10.1111/j.1399-0039.2008.01193.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Coeliac disease (CD) is an autoimmune disorder characterised by inflammation, villous atrophy and hyperplasia of the small intestinal mucosa that affects genetically susceptible individuals. A genome-wide scan was performed in 17 family members with high incidence of CD. Highest nonparametric linkage (NPL) and logarithm of odds (LOD) scores were of 6.21 (P = 0.0107) and 2.57, respectively, to a region on chromosome 11p13-12. Following fine mapping, NPL and LOD scores did not change, but the linkage interval on chromosome 11 was narrowed to a region that is approximately 50.94 cM from pTer. Two inherited haplotypes on chromosomes 11p13-12 and 9q21 were observed in all affected members but not in the majority of clinically normal individuals. Sequencing of genes at region 11p13-12 showed a number of sequence variants, two of which were linked with the inherited haplotype. One of these variants in the CD59 gene was found at a very low frequency in the population and could possibly affect pre-messenger RNA splicing. This study is of particular importance for the identification of novel genes that might be responsible for CD other than human leukocyte antigen.
Collapse
Affiliation(s)
- C Vidal
- Laboratory of Molecular Genetics, Department of Physiology and Biochemistry, University of Malta, Msida, Malta
| | | | | | | |
Collapse
|
13
|
Symposium on 'The challenge of translating nutrition research into public health nutrition'. Session 3: Joint Nutrition Society and Irish Nutrition and Dietetic Institute Symposium on 'Nutrition and autoimmune disease'. Recent advances in genetic understanding of coeliac disease. Proc Nutr Soc 2009; 68:122-6. [PMID: 19243665 DOI: 10.1017/s0029665109001074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Over the past 20 years major advances have been made in the diagnosis and understanding of pathogenic mechanisms relating to coeliac disease. Recently-identified genetic markers support the immunological-inflammatory nature of the disease. It is hoped that these newly-identified genes will assist further dissection of the inflammatory pathways in coeliac disease and give insight into why certain individuals develop intolerance to dietary gluten.
Collapse
|
14
|
The shared CTLA4-ICOS risk locus in celiac disease, IgA deficiency and common variable immunodeficiency. Genes Immun 2008; 10:151-61. [DOI: 10.1038/gene.2008.89] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
15
|
Butty V, Campbell C, Mathis D, Benoist C. Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1). Diabetes 2008; 57:2348-59. [PMID: 18556337 PMCID: PMC2518486 DOI: 10.2337/db07-1736] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 06/05/2008] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The unfolding of type 1 diabetes involves a number of steps: defective immunological tolerance, priming of anti-islet autoimmunity, and destruction of insulin-producing beta-cells. A number of genetic loci contribute to susceptibility to type 1 diabetes, but it is unclear which stages of the disease are influenced by the different loci. Here, we analyzed the frequency of type 1 diabetes-risk alleles among individuals from the Diabetes Prevention Trial-Type 1 (DPT-1) clinical trial, which tested a preventive effect of insulin in at-risk relatives of diabetic individuals, all of which presented with autoimmune manifestations but only one-third of which eventually progressed to diabetes. RESEARCH DESIGN AND METHODS In this study, 708 individuals randomized into DPT-1 were genotyped for 37 single nucleotide polymorphisms in diabetes susceptibility loci. RESULTS Susceptibility alleles at loci expected to influence immunoregulation (PTPN22, CTLA4, and IL2RA) did not differ between progressors and nonprogressors but were elevated in both groups relative to general population frequencies, as was the INS promoter variant. In contrast, HLA DQB1*0302 and DQB1*0301 differed significantly in progressors versus nonprogressors (DQB*0302, 42.6 vs. 34.7%, P = 0.0047; DQB*0301, 8.6 vs. 14.3%, P = 0.0026). Multivariate analysis of the factors contributing to progression demonstrated that initial titers of anti-insulin autoantibodies (IAAs) could account for some (P = 0.0016) but not all of this effect on progression (P = 0.00038 for the independent effect of the number of DQB*0302 alleles). The INS-23 genotype was most strongly associated with anti-IAAs (median IAA levels in TT individuals, 60 nU/ml; AT, 121; and AA, 192; P = 0.000037) and only suggestively to the outcome of oral insulin administration. CONCLUSIONS With the exception of HLA, most susceptibility loci tested condition the risk of autoimmunity rather than the risk of failed immunoregulation that results in islet destruction. Future clinical trials might consider genotyping INS-23 in addition to HLA alleles as disease/treatment response modifier.
Collapse
Affiliation(s)
- Vincent Butty
- From the Section on Immunology and Immunogenetics, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher Campbell
- From the Section on Immunology and Immunogenetics, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Diane Mathis
- From the Section on Immunology and Immunogenetics, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christophe Benoist
- From the Section on Immunology and Immunogenetics, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | |
Collapse
|
16
|
PAVLOVA A, DIAZ-LACAVA A, ZEITLER H, SATOGUINA J, NIEMANN B, KRAUSE M, SCHARRER I, HOERAUF A, WIENKER T, OLDENBURG J. Increased frequency of the CTLA-4 49 A/G polymorphism in patients with acquired haemophilia A compared to healthy controls. Haemophilia 2008; 14:355-60. [DOI: 10.1111/j.1365-2516.2007.01618.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
17
|
Capilla A, Donat E, Planelles D, Espinós C, Ribes-Koninckx C, Palau F. Genetic analyses of celiac disease in a Spanish population confirm association with CELIAC3 but not with CELIAC4. ACTA ACUST UNITED AC 2007; 70:324-9. [PMID: 17767555 DOI: 10.1111/j.1399-0039.2007.00899.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic predisposition to celiac disease (CD) is determined primarily by the human leukocyte antigen (HLA) genes (CELIAC1 region; 6p21), although many loci are involved in disease susceptibility. First, we have analysed a large series of CD patients from the Spanish Mediterranean region who had previously been characterised for the HLA complex. We have investigated how relevant regions contribute to CD susceptibility: CELIAC3 (CD28/CTLA4/ICOS region on 2q33) and CELIAC4 (19p13) as well as the tumour necrosis factor alpha (TNF-alpha) and the linfotoxin loci by case-control and association analyses. We highlight the association with the +49*A allele of cytotoxic T-lymphocyte-associated antigen 4 locus (P = 0.01), and the -308*A of TNF-alpha locus (P = 0.0008) in DQ2 individuals, although an independent role for TNF-alpha as risk factor has not been proven. Moreover, we do not confirm the association with the CELIAC4 region polymorphisms described in other populations.
Collapse
Affiliation(s)
- A Capilla
- Laboratory of Genetics and Molecular Medicine, Instituto de Biomedicina, Consejo Superior de Investigaciones Científicas, c/Jaume Roig 11, 46010 Valencia, Spain
| | | | | | | | | | | |
Collapse
|
18
|
Naluai AT, Ascher H, Nilsson S, Wahlström J. Searching for genes influencing a complex disease: the case of coeliac disease. Eur J Hum Genet 2007; 16:542-53. [PMID: 17726483 DOI: 10.1038/sj.ejhg.5201918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Recently, a few genes have been reported to be causative in inflammatory diseases. Still, we are waiting for the vast majority to be discovered. New tools for genotyping and statistical analysis have been developed and emphasis has been put on study design. Coeliac disease (CD) is a disorder, where prolamins in dietary wheat gluten and related proteins from rye or barley are not tolerated. It is one of the most common chronic diseases in humans exceeding a population prevalence of 1%. In this article, we will summarise what is currently known about the genetics influencing CD with the emphasis on the non-HLA genetic component. We will discuss some difficulties when searching for susceptibility genes in disorders with complex inheritance patterns.
Collapse
Affiliation(s)
- Asa Torinsson Naluai
- Department of Genomics, The Sahlgrenska Academy, Göteborg University, Göteborg, Sweden.
| | | | | | | |
Collapse
|
19
|
Butty V, Roy M, Sabeti P, Besse W, Benoist C, Mathis D. Signatures of strong population differentiation shape extended haplotypes across the human CD28, CTLA4, and ICOS costimulatory genes. Proc Natl Acad Sci U S A 2006; 104:570-5. [PMID: 17197413 PMCID: PMC1766426 DOI: 10.1073/pnas.0610124104] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The three members of the costimulatory receptor family, CD28, CTLA-4, and ICOS, have complementary effects on T cell activation, and their balance controls the overall outcome of immune and autoimmune responses. They are encoded in a short genomic interval, and overall activity may result from interplay between allelic variants at each locus. With multiethnic DNA panels that represent a wide spectrum of human populations, we demonstrate long-range linkage disequilibrium among the three genes. A large fraction of the variation found in the locus can be explained by the presence of extended haplotypes encompassing variants at CD28, CTLA4, and the ICOS promoter. There are unusual differences in the distribution of some variants and haplotypes between geographic regions. The differences may reflect demographic events and/or the adaptation to diverse environmental and microbial challenges encountered in the course of human migrations and will be important to consider when interpreting association to immune/autoimmune responsiveness.
Collapse
Affiliation(s)
| | | | | | | | - Christophe Benoist
- To whom correspondence should be addressed at:
Section on Immunology and Immunogenetics, Joslin Diabetes Center, One Joslin Place, Boston, MA 02215. E-mail:
| | - Diane Mathis
- To whom correspondence should be addressed at:
Section on Immunology and Immunogenetics, Joslin Diabetes Center, One Joslin Place, Boston, MA 02215. E-mail:
| |
Collapse
|
20
|
Shilling RA, Bandukwala HS, Sperling AI. Regulation of T:B cell interactions by the inducible costimulator molecule: does ICOS "induce" disease? Clin Immunol 2006; 121:13-8. [PMID: 16790364 DOI: 10.1016/j.clim.2006.04.574] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 04/27/2006] [Accepted: 04/28/2006] [Indexed: 01/28/2023]
Abstract
The Inducible Costimulator molecule (ICOS), a member of the CD28 family of costimulatory molecules, was identified in 1999 as a molecule expressed primarily on activated human T cells. Induced upon activation, ICOS appears to be an ideal target for modifying T-cell-mediated immune responses. ICOS was also found to be highly expressed on germinal center T cells, suggesting that ICOS was involved in T:B cell interactions. While ICOS has subsequently been shown to be important for both Th1 and Th2 cell activation and effector function, a central role for ICOS in the generation and maintenance of humoral immunity is emerging. In this review, we summarize the evidence that the level of ICOS expression regulates T-cell-dependent B cell responses and propose a model for the role of ICOS in diseases characterized by dysregulated humoral immunity.
Collapse
Affiliation(s)
- Rebecca A Shilling
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago MC 6076, 5841 S. Maryland Ave, Chicago, IL 60637, USA.
| | | | | |
Collapse
|