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Siddique I, Mustafa AS, Khan I, Ziyab AH, Altarrah M, Sulaiman R, Kadungothayil N, Shaheed F. Detection of mutations in NOD2/CARD15 gene in Arab patients with Crohn's disease. Saudi J Gastroenterol 2021; 27:240-248. [PMID: 34380868 PMCID: PMC8448013 DOI: 10.4103/sjg.sjg_582_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Mutations in NOD2/CARD15 gene have been linked to an increased risk of Crohn's disease (CD). The objective of this study is to determine NOD2/CARD15 gene mutations, and their association with the risk of CD in Arabs in Kuwait. METHODS Four NOD2 gene mutations, including Pro268Ser (SNP5), Arg702Trp (SNP8), Gly908Arg (SNP12), and Leu1007FsinsC (SNP13) were examined in Arab CD patients (n = 103) and control subjects (n = 100). The genomic DNA was isolated and used in polymerase chain reaction (PCR) with four sets of specific primers. The PCR-amplified DNA fragments were sequenced and analyzed for the NOD2 mutations. Logistic regression was used to estimate the adjusted odds ratios (aOR) and 95% confidence intervals (CI). RESULTS Of the four genotyped variants, the Arg702Trp (SNP8) and Leu1007FsinsC (SNP13) variants were not informative in our study sample due to minor allele frequency of <1%. The Pro268Ser (SNP5) mutation was detected in 17 (16.5%) CD patients and 32 (32.0%) controls. The Gly908Arg (SNP12) mutation was observed in 24 (23.3%) patients and 10 (10.0%) controls. In the dominant genetic risk model (i.e. carrying at least one minor allele), CD patients compared to controls were less likely to carry either the "CT" or "TT" genotype of variant Pro268Ser (SNP5; aOR = 0.43, 95% CI: 0.22-0.84). In contrast, CD patients compared to controls were more likely to carry the homozygous for the minor allele or the heterozygous genotypes of variant Gly908Arg (SNP12; aOR = 2.67, 95% CI: 1.19-5.97). CONCLUSIONS In this Arab population, carrying at least one copy of the minor allele of Gly908Arg (SNP12) mutation in NOD2 gene was associated with increased susceptibility to CD, while having the heterozygous or homozygous for the minor allele genotype of the Pro268Ser (SNP5) mutation provided protection against CD. Mutations in Arg702Trp (SNP8) and Leu1007FsinsC (SNP13) were not detected in this sample of the Arab population in Kuwait.
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Affiliation(s)
- Iqbal Siddique
- Department of Medicine, Faculty of Medicine, Kuwait University, Kuwait City, Al-Amiri Hospital, Kuwait,Thunayan Al-Ghanim Gastroenterology Center, Al-Amiri Hospital, Kuwait,Address for correspondence: Prof. Iqbal Siddique, Department of Medicine, Faculty of Medicine, Kuwait University, P. O. Box 24923, Safat - 13110, Kuwait. E-mail:
| | - Abu S. Mustafa
- Department of Microbiology, OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait,Department of Research Core Facility, OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Islam Khan
- Department of Biochemistry, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Ali H. Ziyab
- Department of Community Medicine and Behavioral Sciences, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Munira Altarrah
- Thunayan Al-Ghanim Gastroenterology Center, Al-Amiri Hospital, Kuwait
| | - Riyas Sulaiman
- Department of Research Core Facility, OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Numeer Kadungothayil
- Department of Research Core Facility, OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Faraz Shaheed
- Department of Research Core Facility, OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
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Abdelnaby H, Ndiaye NC, D'Amico F, Fouad AM, Hassan S, Elshafey A, Al Hashash W, Faisal M, Alshamali Y, Al-Taweel T, Peyrin-Biroulet L. NOD2/CARD15 polymorphisms (P268S, IVS8 +158, G908R, L1007fs, R702W) among Kuwaiti patients with Crohn's disease: A case-control study. Saudi J Gastroenterol 2021; 27:249-256. [PMID: 34341249 PMCID: PMC8448012 DOI: 10.4103/sjg.sjg_613_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Nucleotide-binding oligomerization domain-containing two (NOD2/CARD15) gene polymorphisms are implicated in the pathogenesis of Crohn's disease (CD). AIM To describe the allelic frequency of NOD2/CARD15 gene variants among Kuwaiti patients with CD and investigate potential genotype/phenotype associations. METHODS Adult Kuwaiti citizens with an established diagnosis of CD and healthy controls were enrolled from October 2018 to May 2020. Three common NOD2/CARD15 polymorphisms (R702W, G908R, and L1007fs) and P268S and IVS8+158 polymorphisms were screened by polymerase chain reaction/restriction analysis length polymorphism (PCR/RFLP). RESULTS Ninety adult Kuwaiti patients with CD and 210 healthy subjects (as controls) were recruited. P268S, IVS8+158, G908R, and R702W minor alleles were identified in 38.9%, 21.1%, 12.2%, and 4.4% of CD patients, respectively. NOD2/CARD15 polymorphisms coexisted in 35 healthy controls (16.7%) and 21 CD patients (23.3%). Individuals with either a single or multiple polymorphism were approximately two times more likely to have CD than those with no polymorphism. Patients with multiple polymorphisms had significantly more stricturing and penetrating disease. CONCLUSION NOD2/CARD15 gene polymorphisms were significantly associated with an increased risk of disease and aggressive phenotypes among the Kuwaiti CD population.
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Affiliation(s)
- Hassan Abdelnaby
- Department of Endemic and Infectious Diseases, Suez Canal University, Ismailia, Egypt,Department of Internal Medicine, Division of Gastroenterology, Al Sabah Hospital, Ministry of Health, Kuwait,Address for correspondence: Dr. Hassan Abdelnaby, Department of Internal Medicine, Division of Gastroenterology, Al Sabah Hospital, Ministry of Health, P.O. Box (5) 13001 Safat,. E-mail:
| | - Ndeye Coumba Ndiaye
- Inserm U1256 « Nutrition – Genetics and Exposure to Environmental Risks - NGERE », University of Lorraine, Vandoeuvre-les-Nancy, France
| | - Ferdinando D'Amico
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Ahmed Mahmoud Fouad
- Department of Public Health, Occupational and Environmental Medicine, Ismailia, Italy
| | - Sameh Hassan
- Department of Internal Medicine, Division of Gastroenterology, Al Sabah Hospital, Ministry of Health, Kuwait
| | - Alaa Elshafey
- Medical Genetics, Pediatric Department, Menofia University, Egypt,Kuwait Medical Genetic Centre, Ministry of Health, Kuwait
| | - Wafaa Al Hashash
- Department of Internal Medicine, Division of Gastroenterology, Al Sabah Hospital, Ministry of Health, Kuwait
| | - Mohammed Faisal
- Surgical Oncology Unit, Department of Surgery, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Yousef Alshamali
- Department of Internal Medicine, Division of Gastroenterology, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait
| | - Talal Al-Taweel
- Department of Internal Medicine, Division of Gastroenterology, Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait
| | - Laurent Peyrin-Biroulet
- Inserm U1256 « Nutrition – Genetics and Exposure to Environmental Risks - NGERE », University of Lorraine, Vandoeuvre-les-Nancy, France,InsermU954, Department of Gastroenterology, Nancy University Hospital, University of Lorraine, Vandoeuvre Les Nancy, France
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Ben Abdelghani K, Gzam Y, Fazaa A, Miladi S, Sellami M, Souabni L, Kassab S, Chekili S, Zakraoui L, Laater A. Non-radiographic axial spondyloarthritis in Tunisia: main characteristics and detailed comparison with ankylosing spondylitis. Clin Rheumatol 2020; 40:1361-1367. [PMID: 32974836 DOI: 10.1007/s10067-020-05415-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/25/2020] [Accepted: 09/16/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The aim of the present study is to compare the clinical features, disease activity, and physical impairment between non-radiographic axial spondyloarthritis and ankylosing spondylitis in Tunisian patients. METHODS This is a retrospective study conducted in a single rheumatology center in Tunisia. Patients with axial spondyloarthritis fulfilling the 2009 ASAS criteria were included. The various spondyloarthritis-related variables were compared between non-radiographic axial spondyloarthritis and ankylosing spondylitis. p Values below 0.05 were considered statistically significant. RESULTS Among 200 patients with axial spondyloarthritis, 40 had non-radiographic axial spondyloarthritis and 160 had ankylosing spondylitis. The non-radiographic axial spondyloarthritis patients were more frequently female, were younger, and had shorter disease duration. Patients with non-radiographic axial spondyloarthritis experienced enthesitis more frequently compared with ankylosing spondylitis patients. Psoriasis was more frequent in non-radiographic axial spondyloarthritis group, while inflammatory bowel disease was more frequent in ankylosing spondylitis group. The C-reactive protein level and functional score were significantly higher in patients with ankylosing spondylitis compared with non-radiographic axial spondyloarthritis. Tumor necrosis factor inhibitors were offered significantly more often to the ankylosing spondylitis group. There was no statistically significant difference between the 2 groups in other spondyloarthritis parameters. CONCLUSION The non-radiographic axial spondyloarthritis is characterized mainly by a marked female prevalence, a higher enthesitis prevalence, and a better physical function. KEY POINTS • Patients with nr-axSpA in Tunisia are more frequently female and have shorter disease duration compared with those with AS. • Peripheral manifestations were similar between nr-axSpA and AS patients except for enthesitis which were more frequent within nr-axSpA patients. • The disease activity is similar between the 2 groups of axSpA but the physical function is better within nr-axSpA patients.
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Affiliation(s)
- Kawther Ben Abdelghani
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia.,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia
| | - Yosra Gzam
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia. .,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia.
| | - Alia Fazaa
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia.,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia
| | - Saoussen Miladi
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia.,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia
| | - Meriem Sellami
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia.,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia
| | - Leila Souabni
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia.,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia
| | - Selma Kassab
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia.,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia
| | - Selma Chekili
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia.,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia
| | - Leith Zakraoui
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia.,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia
| | - Ahmed Laater
- Rheumatology Department, Mongi Slim Hospital, La Marsa, Tunisia.,Faculty of Medecine, University of Tunis el Manar, Tunis, Tunisia
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Targeted Gene Sequencing in Children with Crohn's Disease and Their Parents: Implications for Missing Heritability. G3-GENES GENOMES GENETICS 2018; 8:2881-2888. [PMID: 30166421 PMCID: PMC6118318 DOI: 10.1534/g3.118.200404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Crohn’s disease is a complex genetic trait characterized by chronic relapsing intestinal inflammation. Genome wide association studies (GWAS) have identified more than 170 loci associated with the disease, accounting for ∼14% of the disease variance. We hypothesized that rare genetic variation in GWAS positional candidates also contribute to disease pathogenesis. We performed targeted, massively-parallel sequencing of 101 genes in 205 children with Crohn’s disease, including 179 parent-child trios and 200 controls, both of European ancestry. We used the gene burden test implemented in VAAST and estimated effect sizes using logistic regression and meta-analyses. We identified three genes with nominally significant p-values: NOD2, RTKN2, and MGAT3. Only NOD2 was significant after correcting for multiple comparisons. We identified eight novel rare variants in NOD2 that are likely disease-associated. Incorporation of rare variation and compound heterozygosity nominally increased the proportion of variance explained from 0.074 to 0.089. We estimated the population attributable risk and total heritability of variation in NOD2 to be 32.9% and 3.4%, respectively, with 3.7% and 0.25% accounted for by rare putatively functional variants. Sequencing probands (as opposed to genotyping) to identify rare variants and incorporating phase by sequencing parents can recover a portion of the missing heritability of Crohn’s disease.
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Feki S, Bouzid D, Abida O, Chtourou L, Elloumi N, Toumi A, Hachicha H, Amouri A, Tahri N, Masmoudi H. Genetic association and phenotypic correlation of TLR4 but not NOD2 variants with Tunisian inflammatory bowel disease. J Dig Dis 2017; 18:625-633. [PMID: 29055077 DOI: 10.1111/1751-2980.12552] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/29/2017] [Accepted: 10/15/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The common association between NOD2/CARD15 and TLR4 gene variants with inflammatory bowel disease (IBD) has not been replicated in all studies. We studied the polymorphism of these two genes in Tunisian patients with IBD. METHODS Polymorphisms of NOD2 (R702W, G908R and L1007fs) and TLR4 (Asp299Gly and Thr399Ile) genes were analyzed in 106 patients with IBD (68 with ulcerative colitis [UC], 38 with Crohn's disease [CD]) and 160 healthy controls using polymerase chain reaction-restriction fragment length polymorphism. Genotypes and phenotypes were correlated. RESULTS The mutated allele of TLR4-Thr399Ile was strongly associated with IBD (9.4% in IBD, 7.4% in UC and 13.2% in CD vs 2.5% in controls; P = 0.0004, 0.014 and 0.00006, respectively). Heterozygous genotypes were significantly more frequent in patients with IBD (17.0%), UC (14.7%) and CD (21.1%) than in controls (5.0%) (P = 0.0012, 0.012 and 0.001, respectively). Interestingly, the wild genotype was found to be protective (odds ratio 0.24). The mutated allele of TLR4-Asp299Gly was more frequent in controls (6.8%) than in patients with IBD (2.9%). A phenotypic correlation of Asp299Gly-AG genotype with arthritis in UC patients was detected (P = 0.003). Regarding the NOD2 gene, the common variations studied were not polymorphic and there was no genetic association with IBD. CONCLUSION The TLR4-Thr399Ile variant was strongly associated with susceptibility to IBD, whereas TLR4-Asp299Gly seems to play a role in the clinical expression of UC. The rarity and non-association of NOD2 mutations with IBD may reveal a genetic characteristic of the population in our region.
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Affiliation(s)
- Sawsan Feki
- Department of Immunology, Habib Bourguiba University Hospital, Sfax, Tunisia
| | - Dorra Bouzid
- Department of Immunology, Habib Bourguiba University Hospital, Sfax, Tunisia
| | - Olfa Abida
- Department of Immunology, Habib Bourguiba University Hospital, Sfax, Tunisia
| | - Lassaad Chtourou
- Department of Gastroenterology, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
| | - Nesrine Elloumi
- Department of Immunology, Habib Bourguiba University Hospital, Sfax, Tunisia
| | - Amina Toumi
- Department of Immunology, Habib Bourguiba University Hospital, Sfax, Tunisia
| | - Hend Hachicha
- Department of Immunology, Habib Bourguiba University Hospital, Sfax, Tunisia
| | - Ali Amouri
- Department of Gastroenterology, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
| | - Nabil Tahri
- Department of Gastroenterology, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
| | - Hatem Masmoudi
- Department of Immunology, Habib Bourguiba University Hospital, Sfax, Tunisia
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Zanetti D, Via M, Carreras-Torres R, Esteban E, Chaabani H, Anaibar F, Harich N, Habbal R, Ghalim N, Moral P. Analysis of Genomic Regions Associated With Coronary Artery Disease Reveals Continent-Specific Single Nucleotide Polymorphisms in North African Populations. J Epidemiol 2016; 26:264-71. [PMID: 26780859 PMCID: PMC4848325 DOI: 10.2188/jea.je20150034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background In recent years, several genomic regions have been robustly associated with coronary artery disease (CAD) in different genome-wide association studies (GWASs) conducted mainly in people of European descent. These kinds of data are lacking in African populations, even though heart diseases are a major cause of premature death and disability. Methods Here, 384 single nucleotide polymorphisms (SNPs) in the top four CAD risk regions (1p13, 1q41, 9p21, and 10q11) were genotyped in 274 case-control samples from Morocco and Tunisia, with the aim of analyzing for the first time if the associations found in European populations were transferable to North Africans. Results The results indicate that, as in Europe, these four genetic regions are also important for CAD risk in North Africa. However, the individual SNPs associated with CAD in Africa are different from those identified in Europe in most cases (1p13, 1q41, and 9p21). Moreover, the seven risk variants identified in North Africans are efficient in discriminating between cases and controls in North African populations, but not in European populations. Conclusions This study indicates a disparity in markers associated to CAD susceptibility between North Africans and Europeans that may be related to population differences in the chromosomal architecture of these risk regions.
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Affiliation(s)
- Daniela Zanetti
- Department of Animal Biology-Anthropology, University of Barcelona
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Meddour Y, Chaib S, Bousseloub A, Kaddache N, Kecili L, Gamar L, Nakkemouche M, Djidjik R, Abbadi MC, Charron D, Boucekkine TE, Tamouza R. NOD2/CARD15 and IL23R genetic variability in 204 Algerian Crohn's disease. Clin Res Hepatol Gastroenterol 2014; 38:499-504. [PMID: 24679666 DOI: 10.1016/j.clinre.2014.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/15/2014] [Accepted: 02/11/2014] [Indexed: 02/04/2023]
Abstract
NOD2/CARD15 and IL23R gene variants play an important role in the susceptibility to Crohn's disease (CD). Studies of genotype-phenotype relationship suggest that these variants are associated with the development of the disease and specific phenotype. Preliminary reports analyzing the association between these variants have never been made on Algerian CD's. In a case-control design, 204 Algerian with CD diagnosed for at least 5years and 201 controls were included were genotyped for single nucleotide polymorphisms (SNP) in the NOD2/CARD15 gene R702W (SNP8, rs2066844), G908R (SNP12, rs2066845) and IL23R R381Q (rs11209026) gene variants were determined using the TaqMan SNP genotyping assays. NOD2/CARD15 908R was carried by 3% of the patients and none in control subjects (χ(2)=8.6, Pc=0.003, OR=13.20). NOD2/CARD15 702W was associated to CD outcome (χ(2)=17.2, Pc=0.00003, OR=12.5) and early onset of disease (group A1, χ(2)=19.3, Pc=1.10(-5), OR=14.05, PM-H=2.10(-6)). IL23R 381Q variants was more frequent in CD's patients than controls (χ(2)=8, Pc=0.005, OR=3.48), it was associated to earlier onset (group A1, χ(2)=7.1, Pc=0.007, OR=1.04, PM-H=0.002), extra-intestinal manifestations (EIM) outcome (χ(2)=10.6, Pc=0.001, OR=1.05, PM-H=0.002) and ileocolonic location (χ(2)=6.8, Pc=0.009, OR=1.05, PM-H=0.001). In this Algerian cohort, NOD2/CARD15 and IL23R variants were associated with CD's outcomes and linked to a particular clinical phenotype.
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Affiliation(s)
- Y Meddour
- Immunology Department, Central Hospital of Army, Algiers, Algeria
| | - S Chaib
- Immunology Department, Central Hospital of Army, Algiers, Algeria
| | - A Bousseloub
- Gastroenterology Department, Central Hospital of Army, Algiers, Algeria
| | - N Kaddache
- Gastroenterology Department, Mustapha Bacha Hospital, Algiers, Algeria
| | - L Kecili
- Gastroenterology Department, Mustapha Bacha Hospital, Algiers, Algeria
| | - L Gamar
- Gastroenterology Department, Mustapha Bacha Hospital, Algiers, Algeria
| | - M Nakkemouche
- Gastroenterology Department, Nafissa Hamoud Hospital, Algiers, Algeria
| | - R Djidjik
- Biology Department, Béni-Messous Hospital, Algiers, Algeria; Immunogenetics and Immunopathology Research Laboratory, Algiers, Algeria.
| | - M C Abbadi
- Immunology Department, Pasteur Institute, Algiers, Algeria; Immunogenetics and Immunopathology Research Laboratory, Algiers, Algeria
| | - D Charron
- Immunology and Histocompatibility Department, CIB-HOB, AP-HP, IUH and INSERM UMRS940, Saint-Louis Hospital, Paris, France
| | - T E Boucekkine
- Gastroenterology Department, Mustapha Bacha Hospital, Algiers, Algeria
| | - R Tamouza
- Immunology and Histocompatibility Department, CIB-HOB, AP-HP, IUH and INSERM UMRS940, Saint-Louis Hospital, Paris, France
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NOD2 gene mutations associate weakly with ulcerative colitis but not with Crohn's disease in Indian patients with inflammatory bowel disease. Gene 2012; 512:309-13. [PMID: 23085276 DOI: 10.1016/j.gene.2012.10.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/05/2012] [Accepted: 10/09/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND Three mutations (two missense and one frameshift) in the NOD2 gene are associated with Crohn's disease (CD) in a proportion of patients with Crohn's disease in North America, Europe and Australia. These three mutations are not found in Indian patients with CD. We undertook new studies to identify polymorphisms in the NOD2 gene in the Indian population and to detect whether any of these were associated with inflammatory bowel disease (IBD) in this population. METHODS Individual exons of the NOD2 gene were amplified by PCR and subjected to denaturing high performance liquid chromatography (DHPLC) to detect heteroduplex formation. All 12 exons of the NOD2 gene were amplified and Sanger-sequenced to detect polymorphisms in the NOD2 gene. 310 patients with CD, 318 patients with ulcerative colitis (UC) and 442 healthy controls (HC) were recruited for association studies. DNA from these participants was evaluated for the identified eight polymorphisms by Sequenom analysis. RESULTS Heteroduplex formation was noted by DHPLC in exons 2 and 4 of the NOD2 gene. Sequencing of the entire NOD2 gene data revealed eight polymorphisms - rs2067085, rs2066842, rs2066843, rs1861759, rs2111235, rs5743266, rs2076753, and rs5743291 - of which the latter four were described for the first time in Indians. None of these polymorphisms was associated with CD. The SNPs rs2066842 and rs2066843 were in significant linkage disequilibrium. Both SNPs showed a significant association with UC (P=0.03 and 0.04 respectively; odds ratio 1.44 and 1.41 respectively). CONCLUSION Four NOD2 polymorphisms were identified for the first time in the Indian population. Of 8 NOD2 polymorphisms, none were associated with CD but two were weakly associated with UC. NOD2 polymorphisms do not play a major role in CD genesis in India.
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