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Reshef YA, Finucane HK, Kelley DR, Gusev A, Kotliar D, Ulirsch JC, Hormozdiari F, Nasser J, O'Connor L, van de Geijn B, Loh PR, Grossman SR, Bhatia G, Gazal S, Palamara PF, Pinello L, Patterson N, Adams RP, Price AL. Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. Nat Genet 2018; 50:1483-1493. [PMID: 30177862 PMCID: PMC6202062 DOI: 10.1038/s41588-018-0196-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 07/11/2018] [Indexed: 12/19/2022]
Abstract
Biological interpretation of genome-wide association study data frequently involves assessing whether SNPs linked to a biological process, for example, binding of a transcription factor, show unsigned enrichment for disease signal. However, signed annotations quantifying whether each SNP allele promotes or hinders the biological process can enable stronger statements about disease mechanism. We introduce a method, signed linkage disequilibrium profile regression, for detecting genome-wide directional effects of signed functional annotations on disease risk. We validate the method via simulations and application to molecular quantitative trait loci in blood, recovering known transcriptional regulators. We apply the method to expression quantitative trait loci in 48 Genotype-Tissue Expression tissues, identifying 651 transcription factor-tissue associations including 30 with robust evidence of tissue specificity. We apply the method to 46 diseases and complex traits (average n = 290 K), identifying 77 annotation-trait associations representing 12 independent transcription factor-trait associations, and characterize the underlying transcriptional programs using gene-set enrichment analyses. Our results implicate new causal disease genes and new disease mechanisms.
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Affiliation(s)
- Yakir A Reshef
- Department of Computer Science, Harvard University, Cambridge, MA, USA.
- Harvard/MIT MD/PhD Program, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | | | - David R Kelley
- California Life Sciences LLC, South San Francisco, CA, USA
| | | | - Dylan Kotliar
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob C Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana Farber Cancer Institute, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Farhad Hormozdiari
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luke O'Connor
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA
| | - Bryce van de Geijn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Po-Ru Loh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sharon R Grossman
- Harvard/MIT MD/PhD Program, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gaurav Bhatia
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Steven Gazal
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pier Francesco Palamara
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, University of Oxford, Oxford, UK
| | - Luca Pinello
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | | | - Ryan P Adams
- Google Brain, New York, NY, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Alkes L Price
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Zhou F, Zhu L, Wang K, Murray M. Recent advance in the pharmacogenomics of human Solute Carrier Transporters (SLCs) in drug disposition. Adv Drug Deliv Rev 2017; 116:21-36. [PMID: 27320645 DOI: 10.1016/j.addr.2016.06.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/01/2016] [Accepted: 06/08/2016] [Indexed: 12/11/2022]
Abstract
Drug pharmacokinetics is influenced by the function of metabolising enzymes and influx/efflux transporters. Genetic variability of these genes is known to impact on clinical therapies. Solute Carrier Transporters (SLCs) are the primary influx transporters responsible for the cellular uptake of drug molecules, which consequently, impact on drug efficacy and toxicity. The Organic Anion Transporting Polypeptides (OATPs), Organic Anion Transporters (OATs) and Organic Cation Transporters (OCTs/OCTNs) are the most important SLCs involved in drug disposition. The information regarding the influence of SLC polymorphisms on drug pharmacokinetics is limited and remains a hot topic of pharmaceutical research. This review summarises the recent advance in the pharmacogenomics of SLCs with an emphasis on human OATPs, OATs and OCTs/OCTNs. Our current appreciation of the degree of variability in these transporters may contribute to better understanding the inter-patient variation of therapies and thus, guide the optimisation of clinical treatments.
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Abstract
Organic anions and cations (OAs and OCs, respectively) comprise an extraordinarily diverse array of compounds of physiological, pharmacological, and toxicological importance. The kidney, primarily the renal proximal tubule, plays a critical role in regulating the plasma concentrations of these organic electrolytes and in clearing the body of potentially toxic xenobiotics agents, a process that involves active, transepithelial secretion. This transepithelial transport involves separate entry and exit steps at the basolateral and luminal aspects of renal tubular cells. Basolateral and luminal OA and OC transport reflects the concerted activity of a suite of separate proteins arranged in parallel in each pole of proximal tubule cells. The cloning of multiple members of several distinct transport families, the subsequent characterization of their activity, and their subcellular localization within distinct regions of the kidney, now allows the development of models describing the molecular basis of the renal secretion of OAs and OCs. New information on naturally occurring genetic variation of many of these processes provides insight into the basis of observed variability of drug efficacy and unwanted drug-drug interactions in human populations. The present review examines recent work on these issues.
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Affiliation(s)
- Ryan M Pelis
- Novartis Pharmaceuticals Corp., Translational Sciences, East Hanover, New Jersey, USA
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Tsianos EV, Katsanos KH, Tsianos VE. Role of genetics in the diagnosis and prognosis of Crohn's disease. World J Gastroenterol 2011; 17:5246-59. [PMID: 22219593 PMCID: PMC3247688 DOI: 10.3748/wjg.v17.i48.5246] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/15/2011] [Accepted: 06/22/2011] [Indexed: 02/06/2023] Open
Abstract
Considering the epidemiological, genetic and immunological data, we can conclude that the inflammatory bowel diseases are heterogeneous disorders of multifactorial etiology in which hereditability and environment interact to produce the disease. It is probable that patients have a genetic predisposition for the development of the disease coupled with disturbances in immunoregulation. Several genes have so far been related to the diagnosis of Crohn's disease. These genes are related to innate pattern recognition receptors, to epithelial barrier homeostasis and maintenance of epithelial barrier integrity, to autophagy and to lymphocyte differentiation. So far, the strongest and most replicated associations with Crohn's disease have been demonstrated with NOD2, IL23R and ATG16L1 genes. Many genes have so far been implicated in the prognosis of Crohn's disease and many attempts have been made for classification of genetic profiles in Crohn's disease. CARD15 seems to be not only a susceptibility gene, but also a disease-modifier gene for Crohn's disease. Enriching our understanding of Crohn's disease genetics is of value, but when combining genetic data with functional data the outcome could be of major importance to clinicians.
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Grube M, Ameling S, Noutsias M, Köck K, Triebel I, Bonitz K, Meissner K, Jedlitschky G, Herda LR, Reinthaler M, Rohde M, Hoffmann W, Kühl U, Schultheiss HP, Völker U, Felix SB, Klingel K, Kandolf R, Kroemer HK. Selective regulation of cardiac organic cation transporter novel type 2 (OCTN2) in dilated cardiomyopathy. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 178:2547-59. [PMID: 21641380 DOI: 10.1016/j.ajpath.2011.02.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 02/01/2011] [Accepted: 02/07/2011] [Indexed: 01/11/2023]
Abstract
Organic cation transporters (OCT1-3 and OCTN1/2) facilitate cardiac uptake of endogenous compounds and numerous drugs. Genetic variants of OCTN2, for example, reduce uptake of carnitine, leading to heart failure. Whether expression and function of OCTs and OCTNs are altered by disease has not been explored in detail. We therefore studied cardiac expression, heart failure-dependent regulation, and affinity to cardiovascular drugs of these transporters. Cardiac transporter mRNA levels were OCTN2>OCT3>OCTN1>OCT1 (OCT2 was not detected). Proteins were localized in vascular structures (OCT3/OCTN2/OCTN1) and cardiomyocytes (OCT1/OCTN1). Functional studies revealed a specific drug-interaction profile with pronounced inhibition of OCT1 function, for example, carvedilol [half maximal inhibitory concentration (IC₅₀), 1.4 μmol/L], diltiazem (IC₅₀, 1.7 μmol/L), or propafenone (IC₅₀, 1.0 μmol/L). With use of the cardiomyopathy model of coxsackievirus-infected mice, Octn2mRNA expression was significantly reduced (56% of controls, 8 days after infection). Accordingly, in endomyocardial biopsy specimens OCTN2 expression was significantly reduced in patients with dilated cardiomyopathy, whereas the expression of OCT1-3 and OCTN1 was not affected. For OCTN2 we observed a significant correlation between expression and left ventricular ejection fraction (r = 0.53, P < 0.0001) and the presence of cardiac CD3⁺ T cells (r = -0.45, P < 0.05), respectively. OCT1, OCT3, OCTN1, and OCTN2 are expressed in the human heart and interact with cardiovascular drugs. OCTN2 expression is selectively reduced in dilated cardiomyopathy patients and predicts the impairment of cardiac function.
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Affiliation(s)
- Markus Grube
- Department of Pharmacology, Ernst-Moritz-Arndt University, Greifswald, Germany
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Talián G, Lakner L, Bene J, Komlósi K, Horváth K, Gasztonyi B, Miheller P, Figler M, Mózsik G, Tulassay Z, Melegh B. Plasma carnitine ester profiles in Crohn's disease and ulcerative colitis patients with different IGR2230a_1 genotypes. Int J Immunogenet 2009; 36:329-35. [PMID: 19735486 DOI: 10.1111/j.1744-313x.2009.00834.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
An association has been repeatedly demonstrated between inflammatory bowel disease (IBD) and the IBD5 locus in the 5q31 chromosomal region. The aim of the present study was to examine the prevalence of the IGR2230a_1 intronic nucleotide polymorphism of the slc22a5 gene (coding for the OCTN2 carnitine transporter protein) lying within this region, and its possible relationship with the carnitine metabolism in Hungarian IBD patients and controls. We genotyped by restriction fragment length polymorphism 200 Crohn's disease (CD) and 246 ulcerative colitis (UC) patients, as well as 187 healthy controls. From plasma samples we determined detailed carnitine ester profiles of 76 CD, 43 UC patients and 45 control persons using electrospray ionization triple quadruple tandem mass spectrometry. The distribution of the genotypes was not significantly different in the CD or the UC group compared with the controls. We found no significant alterations of the carnitine profile in the carrier/non-carrier or the homozygote/non-homozygote comparisons in both the CD and the UC groups, stratified by IGR2230a_1 genotype. Our data suggest that this polymorphism alone is not associated with CD and UC in the Hungarian population, and has no effect on the carnitine metabolism.
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Affiliation(s)
- G Talián
- Department of Medical Genetics and Child Development, University of Pécs, H-7624 Pécs, Hungary
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Magyari L, Melegh B. [Susceptibility genetic variants in Hungarian morbus Crohn and ulcerative colitis patients]. Orv Hetil 2009; 150:81-8. [PMID: 19103559 DOI: 10.1556/oh.2009.28445] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We examined several susceptibility genetic variants to inflammatory bowel disease (Crohn's disease, ulcerative colitis) in Hungarian population, such as the CARD15 R702W, G908R, 1007finsC genetic variants, the SLC22A4 C1672T and SLC22A5 G-207C variants and their determined TC haplotype, the CTLA4 gene A+49G genetic variant and the rs10889677 C/A, rs2201841 T/C, rs1884444 G/T variants of the IL23R gene. We examined 201 adult patients with Crohn's disease, 241 adult patients with ulcerative colitis and 19 pediatric patients with Crohn's disease. For control 235 adult and 49 pediatric subjects were used. The genotyping was carried out using PCR/RFLP methods and direct sequencing. From the CARD15 gene mutations in the adult Crohn's disease population the 1007finsC, while in the pediatric population the 1007finsC and the G908R were significantly associated with an increased risk for Crohn's disease. We found no significant differences comparing the results of the patients and the controls by the SLC22A4, SLC22A5 genetic variants and the TC haplotype. The A+49G variant of the CTLA4 gene was not an independent determinant to inflammatory bowel disease. We found that the IL23R gene variants, rs10889677 C/A and rs2201841 T/C appear to increase susceptibility to Crohn's disease. It depends on the different populations whether this genetic variant means an obligatory risk factor to inflammatory bowel disease.
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Affiliation(s)
- Lili Magyari
- Pécsi Tudományegyetem, Altalános Orvostudományi Kar, Orvosi Genetikai és Gyermekfejlodéstani Intézet, Pécs
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Miyairi I, DeVincenzo JP. Human genetic factors and respiratory syncytial virus disease severity. Clin Microbiol Rev 2008; 21:686-703. [PMID: 18854487 PMCID: PMC2570150 DOI: 10.1128/cmr.00017-08] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
SUMMARY To explain the wide spectrum of disease severity caused by respiratory syncytial virus (RSV) and because of the limitations of animal models to fully parallel human RSV disease, study of genetic influences on human RSV disease severity has begun. Candidate gene approaches have demonstrated associations of severe RSV in healthy infants with genetic polymorphisms that may alter the innate ability of humans to control RSV (surfactants, Toll-like receptor 4, cell surface adhesion molecules, and others) and those that may control differences in proinflammatory responses or enhanced immunopathology (specific cytokines and their receptors). These studies are reviewed. They are valuable since an understanding of the direction of a polymorphism's effect can help construct a meaningful human RSV disease pathogenesis model. However, the direction, degree, and significance of the statistical association for any given gene are equivocal among studies, and the functional significance of specific polymorphisms is often not even known. Polymorphism frequency distribution differences associated with RSV infection arising from diversity in the genetic background of the population may be confounded further by multiple-hypothesis testing and publication bias, as well as the investigator's perceived importance of a particular pathogenic disease process. Such problems highlight the limitation of the candidate gene approach and the need for an unbiased large-scale genome-wide association study to evaluate this important disease.
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Affiliation(s)
- Isao Miyairi
- Department of Pediatrics, University of Tennessee, Memphis, Tennessee 38103, USA
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Li Y, Chang M, Schrodi SJ, Callis-Duffin KP, Matsunami N, Civello D, Bui N, Catanese JJ, Leppert MF, Krueger GG, Begovich AB. The 5q31 variants associated with psoriasis and Crohn's disease are distinct. Hum Mol Genet 2008; 17:2978-85. [PMID: 18614543 PMCID: PMC2536504 DOI: 10.1093/hmg/ddn196] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Predisposition to psoriasis is known to be affected by genetic variation in HLA-C, IL12B and IL23R, but other genetic risk factors also exist. We recently reported three psoriasis-associated single nucleotide polymorphisms (SNPs) in the 5q31 locus, a region of high linkage disequilibrium laden with inflammatory pathway genes. The aim of this study was to assess whether other variants in the 5q31 region are causal to these SNPs or make independent contributions to psoriasis risk by genotyping a comprehensive set of tagging SNPs in a 725 kb region bounded by IL3 and IL4 and testing for disease association. Ninety SNPs, capturing 86.4% of the genetic diversity, were tested in one case–control sample set (467 cases/460 controls) and significant markers (Pallelic < 0.05) (n = 9) were then tested in two other sample sets (981 cases/925 controls). All nine SNPs were significant in a meta-analysis of the combined sample sets. Pair-wise conditional association tests showed rs1800925, an intergenic SNP located just upstream of IL13 (Mantel–Haenszel Pcombined = 1.5 × 10−4, OR = 0.77 [0.67–0.88]), could account for observed significant association of all but one other SNP, rs11568506 in SLC22A4 [Mantel–Haenszel Pcombined = 0.043, OR = 0.68 (0.47–0.99)]. Haplotype analysis of these two SNPs showed increased significance for the two common haplotypes (rs11568506–rs1800925: GC, Pcombined = 5.67 × 10−6, OR = 1.37; GT, Pcombined = 6.01 × 10−5, OR = 0.75; global haplotype P = 8.93 × 10−5). Several 5q31-region SNPs strongly associated with Crohn's disease (CD) in the recent WTCCC study were not significant in the psoriasis sample sets tested here. These results identify the most significant 5q31 risk variants for psoriasis and suggest that distinct 5q31 variants contribute to CD and psoriasis risk.
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Affiliation(s)
- Yonghong Li
- Celera, 1401 Harbor Bay Parkway, Alameda, CA 94502, USA.
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Zhang H, Massey D, Tremelling M, Parkes M. Genetics of inflammatory bowel disease: clues to pathogenesis. Br Med Bull 2008; 87:17-30. [PMID: 18753178 DOI: 10.1093/bmb/ldn031] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION OR BACKGROUND It has long been recognized from epidemiological data that inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis (UC), have a strong genetic predisposition, interacting with unknown environmental drivers to render susceptible individuals at risk for relapsing intestinal inflammation. Substantial progress has been made in the last 2 years in characterizing the susceptibility genes involved. SOURCES OF DATA The recent acceleration in understanding has resulted from the use of new technologies of genome-wide association scanning in large panels of cases and controls. AREAS OF AGREEMENT Genome scans have robustly identified 11 susceptibility genes and loci and highlighted a number of new, previously unsuspected pathways as playing an important role in IBD pathogenesis-including the IL23 pathway in IBD overall and specific aspects of innate immunity (particularly NOD2 and the autophagy genes ATG16L1 and IRGM) in CD. AREAS OF CONTROVERSY The next challenge is to identify specific causal variants at each of the confirmed susceptibility loci and then characterize their biological impact on gene expression and function of the protein product. GROWING POINTS To date, most attention has focused on CD. A recent meta-analysis has increased the number of confirmed susceptibility loci to 32-more than for any other common disease to date. Attention is now turning to the use of the same techniques in UC to identify new, disease-specific genes and understand areas of overlap. AREAS TIMELY FOR DEVELOPING RESEARCH This review explores genetic clues to the pathogenesis of IBD derived from the growing list of confirmed IBD susceptibility genes, and briefly elaborates some of the important themes and overlaps that are becoming evident both within IBD and also with other complex diseases.
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Affiliation(s)
- Hu Zhang
- IBD Genetics Research Group, Addenbrooke's Hospital, Cambridge University, UK
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Cummings JRF, Ahmad T, Geremia A, Beckly J, Cooney R, Hancock L, Pathan S, Guo C, Cardon LR, Jewell DP. Contribution of the novel inflammatory bowel disease gene IL23R to disease susceptibility and phenotype. Inflamm Bowel Dis 2007; 13:1063-8. [PMID: 17508420 DOI: 10.1002/ibd.20180] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND A North American genome-wide single nucleotide polymorphism (SNP) association study identified IL23R as a novel inflammatory bowel disease (IBD) susceptibility gene. Association was reported with multiple risk variants in the centromeric portion of IL23R in 3 large independent cohorts. The aims of this study were to replicate the association of IL23R with Crohn's disease (CD), examine subphenotype relationships, and look for evidence of epistasis with the known CD susceptibility gene CARD15 and susceptibility haplotype IBD5 in a large collection of CD patients. We further investigated the relationship between IL23R and ulcerative colitis (UC). METHODS In all, 604 CD and 647 UC patients who had been rigorously phenotyped and who had been recruited from a single UK center were used in this study. Controls were either spouses of patients (141) or were recruited from well-person clinics (993). Eight SNPs were genotyped using MassArray (Sequenom). All 8 SNPs genotyped were significantly associated with CD. RESULTS The association with the nonsynonymous SNP rs11209026 was confirmed (P=6.65x10(-6), odds ratio [OR], 0.43, 95% confidence interval [CI]: 0.29-0.64). The most significant SNP in our study was rs7517847 (P=4.9x10(-9), OR 0.65, 0.56-0.75), which is statistically independent of rs11209026. Preliminary evidence suggests an epistatic interaction with the IBD5 risk haplotype. The effects of mutations in this IL23R appear weaker in UC (P=0.008, OR 0.63, 0.45-0.89 and 0.005 OR, 0.81, 0.71-0.94, respectively). No subphenotype associations were identified. CONCLUSIONS We confirmed the findings that IL23R is a susceptibility gene for IBD with suggestive epistasis with the IBD5 locus in the CD population.
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Affiliation(s)
- J R Fraser Cummings
- Wellcome Trust Centre for Human Genetics, University of Oxford, and Gastroenterology Unit, Gibson Laboratories, Radcliffe Infirmary, Oxford, UK.
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Cummings JRF, Cooney R, Pathan S, Anderson CA, Barrett JC, Beckly J, Geremia A, Hancock L, Guo C, Ahmad T, Cardon LR, Jewell DP. Confirmation of the role of ATG16L1 as a Crohn's disease susceptibility gene. Inflamm Bowel Dis 2007; 13:941-6. [PMID: 17455206 DOI: 10.1002/ibd.20162] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND A German genome-wide nonsynonymous single nucleotide polymorphism (nsSNP) association study identified ATG16L1 as a Crohn's disease (CD) susceptibility gene. The association appeared to be confined to the nsSNP rs2,241,880 and was confirmed in 2 German independent case-control collections (combined P = 4.0 x 10(-8), odds ratio [OR] 1.45; 95% confidence interval [CI]: 1.21-1.74), a CD transmission disequilibrium test (TDT) collection, and an independent UK cohort. A weak statistical interaction with CARD15 was demonstrated. No association with ulcerative colitis (UC) was demonstrated. The aims of the study were to replicate the association with CD, examine subphenotype associations and statistical interactions with CARD15, IL23R, and the IBD5 risk haplotype, as well as explore the association with UC. METHODS The study included 645 CD and 676 UC rigorously phenotyped patients recruited from a single UK center. Unaffected controls comprised either spouses of patients (141) or individuals recruited from well-person clinics (1,049). The nsSNP rs2,241,880 was genotyped using MassArray (Sequenom). RESULTS A strong association with CD was demonstrated (P = 2.33 x 10(-7), OR 1.45 [1.25-1.67]), but no significant association was demonstrated with any subphenotype. We failed to replicate the reported interaction between rs2,241,880 and the CARD15 low-risk haplotypes dd and Dd. No significant statistical interaction with the 3 known CD susceptibility genes was seen. No association with UC susceptibility (P = 0.37, OR 1.06 [0.93-1.22]), or any UC subphenotype was identified. CONCLUSIONS We confirmed the findings that ATG16L1 is a CD susceptibility gene and found no evidence of interaction with CARD15, IL23R, or IBD5.
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Affiliation(s)
- J R Fraser Cummings
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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Yamazaki K, Onouchi Y, Takazoe M, Kubo M, Nakamura Y, Hata A. Association analysis of genetic variants in IL23R, ATG16L1 and 5p13.1 loci with Crohn's disease in Japanese patients. J Hum Genet 2007; 52:575-583. [PMID: 17534574 DOI: 10.1007/s10038-007-0156-z] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 04/29/2007] [Indexed: 12/20/2022]
Abstract
Inflammatory bowel diseases, Crohn's disease (CD) and ulcerative colitis are characterised by chronic transmural, segmental and typically granulomatous inflammation of the gut. Each has a peak age of onset in the second to fourth decades of life and prevalence has been increasing significantly in both Western countries and Japan over the last decade, while their pathogenesis remains largely unknown. Recently, positive association of CD with the variants in interleukin 23 receptor (IL23R), autophagy-related 16-like 1 (ATG16L1) genes and chromosome 5p13.1 locus was reported through genome-wide association studies which are now recognised as a robust tool for the identification of susceptibility genes for complex diseases. To examine an association of reported susceptible variants in the three loci with Japanese CD patients, a total of 484 CD patients and 439 controls were genotyped. No evidence of positive association for any of these loci with CD was found in the Japanese population, even after clinically stratified subgroups of CD were used. Our result revealed a distinct ethnic difference of genetic background of CD that we reported previously in other genes between Japanese and Caucasian populations. Further genetic studies are required to confirm our findings with ethnically divergent populations.
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Affiliation(s)
- Keiko Yamazaki
- Laboratory for Gastrointestinal Diseases, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan.
| | - Yoshihiro Onouchi
- Laboratory for Gastrointestinal Diseases, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | - Masakazu Takazoe
- Department of Medicine, Division of Gastroenterology, Social Insurance Chuo General Hospital, Tokyo, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akira Hata
- Laboratory for Gastrointestinal Diseases, SNP Research Center, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
- Department of Public Health, Chiba University Graduate School of Medicine, Chiba, Japan
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Koepsell H, Lips K, Volk C. Polyspecific organic cation transporters: structure, function, physiological roles, and biopharmaceutical implications. Pharm Res 2007. [PMID: 17473959 DOI: 10.1007/s11095‐007‐9254‐z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The body is equipped with broad-specificity transporters for the excretion and distribution of endogeneous organic cations and for the uptake, elimination and distribution of cationic drugs, toxins and environmental waste products. This group of transporters consists of the electrogenic cation transporters OCT1-3 (SLC22A1-3), the cation and carnitine transporters OCTN1 (SLC22A4), OCTN2 (SLC22A5) and OCT6 (SLC22A16), and the proton/cation antiporters MATE1, MATE2-K and MATE2-B. The transporters show broadly overlapping sites of expression in many tissues such as small intestine, liver, kidney, heart, skeletal muscle, placenta, lung, brain, cells of the immune system, and tumors. In epithelial cells they may be located in the basolateral or luminal membranes. Transcellular cation movement in small intestine, kidney and liver is mediated by the combined action of electrogenic OCT-type uptake systems and MATE-type efflux transporters that operate as cation/proton antiporters. Recent data showed that OCT-type transporters participate in the regulation of extracellular concentrations of neurotransmitters in brain, mediate the release of acetylcholine in non-neuronal cholinergic reactions, and are critically involved in the regulation of histamine release from basophils. The recent identification of polymorphisms in human OCTs and OCTNs allows the identification of patients with an increased risk for adverse drug reactions. Transport studies with expressed OCTs will help to optimize pharmacokinetics during development of new drugs.
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Affiliation(s)
- Hermann Koepsell
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University, Würzburg, Germany.
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Koepsell H, Lips K, Volk C. Polyspecific organic cation transporters: structure, function, physiological roles, and biopharmaceutical implications. Pharm Res 2007; 24:1227-51. [PMID: 17473959 DOI: 10.1007/s11095-007-9254-z] [Citation(s) in RCA: 742] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Accepted: 01/26/2007] [Indexed: 12/11/2022]
Abstract
The body is equipped with broad-specificity transporters for the excretion and distribution of endogeneous organic cations and for the uptake, elimination and distribution of cationic drugs, toxins and environmental waste products. This group of transporters consists of the electrogenic cation transporters OCT1-3 (SLC22A1-3), the cation and carnitine transporters OCTN1 (SLC22A4), OCTN2 (SLC22A5) and OCT6 (SLC22A16), and the proton/cation antiporters MATE1, MATE2-K and MATE2-B. The transporters show broadly overlapping sites of expression in many tissues such as small intestine, liver, kidney, heart, skeletal muscle, placenta, lung, brain, cells of the immune system, and tumors. In epithelial cells they may be located in the basolateral or luminal membranes. Transcellular cation movement in small intestine, kidney and liver is mediated by the combined action of electrogenic OCT-type uptake systems and MATE-type efflux transporters that operate as cation/proton antiporters. Recent data showed that OCT-type transporters participate in the regulation of extracellular concentrations of neurotransmitters in brain, mediate the release of acetylcholine in non-neuronal cholinergic reactions, and are critically involved in the regulation of histamine release from basophils. The recent identification of polymorphisms in human OCTs and OCTNs allows the identification of patients with an increased risk for adverse drug reactions. Transport studies with expressed OCTs will help to optimize pharmacokinetics during development of new drugs.
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Affiliation(s)
- Hermann Koepsell
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University, Würzburg, Germany.
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Duerr RH. Genome-wide association studies herald a new era of rapid discoveries in inflammatory bowel disease research. Gastroenterology 2007; 132:2045-9. [PMID: 17484895 DOI: 10.1053/j.gastro.2007.03.082] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Magyari L, Faragó B, Bene J, Horvatovich K, Lakner L, Varga M, Figler M, Gasztonyi B, Mózsik G, Melegh B. No association of the cytotoxic T-lymphocyte associated gene CTLA4 +49A/G polymorphisms with Crohn’s disease and ulcerative colitis in Hungarian population samples. World J Gastroenterol 2007; 13:2205-8. [PMID: 17465502 PMCID: PMC4146845 DOI: 10.3748/wjg.v13.i15.2205] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: The goal of the current work was to analyse the prevalence of the +49A/G variant of the cytotoxic T-lymphocyte antigen 4 gene (CTLA4) in Hungarian patients with Crohn’s disease (CD) and ulcerative colitis (UC).
METHODS: A total of 130 unrelated subjects with CD and 150 with UC, and 170 matched controls were genotyped for the single nucleotide polymorphism (SNP). The genotypes were determined by using PCR/RFLP test.
RESULTS: The G allele frequency and the prevalence of the GG genotype were 38.1% and 12.3% in the CD group, 40.6% and 18.6% in the UC patients, and 37.4% and 15.9% in the control group, respectively.
CONCLUSION: The results of the current study show that carriage of the +49G SNP in heterozygous or in homozygous form does not confer risk either for CD or for UC in the Hungarian population.
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Affiliation(s)
- Lili Magyari
- Department of Medical Genetics and Child Development, University of Pecs, H-7624 Pecs, Szigeti 12, Hungary
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Magyari L, Bene J, Komlósi K, Talián G, Faragó B, Csöngei V, Járomi L, Sáfrány E, Sipeky C, Lakner L, Varga M, Gasztonyi B, Melegh B. Prevalence of SLC22A4 1672T and SLC22A5 −207C combination defined TC haplotype in Hungarian ulcerative colitis patients. Pathol Oncol Res 2007; 13:53-6. [PMID: 17387389 DOI: 10.1007/bf02893441] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Accepted: 12/15/2006] [Indexed: 02/07/2023]
Abstract
Ulcerative colitis (UC) is a chronic inflammatory disease of the gastrointestinal tract. The aim of this study was to verify the prevalence rate of the haplotype called TC, determined by combination of two functional alleles of OCTN cation transporter genes (SLC22A4 1672T and SLC22A5 -207C combination variants) in ulcerative colitis patients and unrelated healthy controls. The "TC haplotype" has recently been suggested to confer risk for UC. A total of 121 unrelated Hungarian subjects with UC and 110 matched controls were genotyped for the two single nucleotide polymorphisms. The genotypes were determined by using PCR/RFLP assay and direct sequencing. The SLC22A4 1672T allele frequency was 46.7% in the patients with UC and 46.4% in the controls, whereas the SLC22A5 -207C allele occurred in 48.8% of the patients and 51.4% of the controls. The prevalence of the TC haplotype was 19% in the patient group and 22.7% in controls. Since there was no accumulation of the TC haplotype in the patient group, our observation suggests that carrying the TC haplotype is not associated with a higher risk for UC in the Hungarian population.
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Affiliation(s)
- Lili Magyari
- Department of Medical Genetics and Child Development, University of Pécs, Pécs, H-7624, Hungary
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