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Lack of the association beetween single nucleotide polymorphism in programmed cell death 1 gene and susceptibility to chronic hepatitis B infection in the Iranian population  [cached]
Hamed Naghoosi,Seyed Reza Mohebbi,Seyed Mohammad Ebrahim Tahaei,Pedram Azimzadeh
Koomesh , 2012,
Abstract: Introduction: Hepatitis B virus (HBV) is one of the most important causative agents of chronic hepaticdiseases worldwide. Along with viral and immunological components, host genetic background includingsingle nucleotide polymorphisms (SNPs) has a critical role on chronicity or clearance of infection.Programmed cell death 1 is an inhibitory receptor which is expressed on virus-specific T cells and impairsthe T cell response in chronic viral infections. In this research the relationship between a single nucleotidepolymorphism of exon 5 of the programmed cell death 1 gene (PD1) and susceptibility to chronic hepatitisB infection in an Iranian population has been studied.Materials and Methods: In such case-control study, genomic DNA from 160 chronic HBV patients and150 healthy controls was extracted and genotyping was performed by PCR-RFLP method.Results: Frequencies of TT, CT and CC genotypes of single nucleotide polymorphism on position 7785of the exon 5 of PD1 gene were %12.5, %40 and %47.5 in patient group and %10.7, %42.7 and %46.6 incontrol group, respectively. No statistically significant difference was seen between case and control groups(p value: 0.832).Conclusion: Although in later studies the relationship between this SNP and susceptibility to someimmunological disorders such as rheumatoid arthritis was observed, results of this study suggest that thereis no association between PD1 exon 5 C/T single nucleotide polymorphism and susceptibility to chronichepatitis B in the Iranian population.
Polymorphism Identification and Association Analysis of IRF3 Gene in Pig
Zhihua Cai,Like Wang,Deyi Liu,Shenghe Li,Xunsheng Pang,Yuxin Cheng
Journal of Animal and Veterinary Advances , 2012, DOI: 10.3923/javaa.2011.1841.1844
Abstract: In this study, IRF3 gene was chosen as a candidate gene for evaluating its effect on porcine immune traits. A SNP (HQ026024: g.4252T>C) in exon7 of IRF3 gene was demonstrated by PCR-SSCP analysis and sequencing. Immune traits including IFN-γ and IL10 concentrations in serum were measured when the pigs are at 20th day of age. The further association analysis of SNP genotypes with immune traits were also conducted in 3 pig breeds including Large white, Landraces and Chinese indigenous breed Dingyuan black pig. The results indicated that the SNP of IRF3 gene had highly significant effects on level of IFN-γ and IL10 (day 20) in serum (p = 0.0344; p = 0.0121) and ratio of IFN-γ to IL10 (day 20) in serum (p = 0.0315). The results suggested that the IRF3 gene could be regarded as a molecular marker gene for genetic selection of these immune traits in the pig breeding program.
Association of Fas -1377 G/A Polymorphism with Susceptibility to Cancer  [PDF]
Peiliang Geng, Jianjun Li, Juanjuan Ou, Ganfeng Xie, Ning Wang, Lisha Xiang, Rina Sa, Chen Liu, Hongtao Li, Houjie Liang
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0088748
Abstract: Background The relationship between Fas -1377 G/A polymorphism and cancer susceptibility has been implicated in accumulating data. However, the data presented inconsistent results. This study was devised to investigate the association of Fas -1377 G/A polymorphism and cancer susceptibility in a large number of participants. Methods The databases of PubMed, Embase, and Web of Science were searched and a total of 27 case-control studies including 13,355 cases and 16,078 controls were included in this meta-analysis. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using the fixed-effects model. Statistical analyses were performed by using Stata software. Results The results suggested that Fas -1377 G/A polymorphism was overall associated with cancer susceptibility (additive model: OR, 1.16, 95%CI = 1.06–1.27, Pheterogeneity = 0.381; recessive model: OR, 1.19, 95%CI = 1.10–1.29, Pheterogeneity = 0.137). In the subgroup analysis by cancer type, significantly increased risk was observed in breast cancer (additive model: OR, 1.24, 95%CI = 1.04–1.58, Pheterogeneity = 0.614; recessive model: OR, 1.24, 95%CI = 1.02–1.51, Pheterogeneity = 0.349) and lung cancer (recessive model: OR, 1.25, 95%CI = 1.04–1.49, Pheterogeneity = 0.090). Similarly, elevated cancer risk associated with Fas -1377 G/A polymorphism was revealed in Asians. Conclusions The combined results suggest that Fas -1377 G/A polymorphism might modulate cancer susceptibility in an Asian-specific manner.
Association of Mannose Binding Lectin Polymorphism with Hepatitis C Infection in Northwest of Iran
Mohammad H. Somi,Mohammad Asgharzadeh,Sara Farhang,Rasoul Estakhry
Hepatitis Monthly , 2006,
Abstract: Background and Aims: Persistent infection with hepatitis C virus leads to liver cirrhosis and often to liver cancer. Mannose binding lectin is a C-type serum lectin, which plays an important role in innate immunity by activating the classical complement pathway. Variants of the mannose binding lectin have been shown to be associated with low serum concentrations of the protein and to predispose the subjects to bacterial, fungal and viral infections. This study was undertaken to investigate the association between hepatitis C virus infection and polymorphisms of mannose binding lectin gene.Methods: We assessed the single nucleotide polymorphism of mannose binding lectin in exon 1, at codon 52, codon 54 and codon 57 in 100 patients infected with hepatitis C virus and 100 controls in Iranian population. Mannose binding lectin gene mutations were determined by means of polymerase chain reaction and restriction fragment length polymorphism analyses.Results: The occurrence of the codon 54 mutation was significantly higher in patients (OR 3.53, CI 95%: 1.94-6.44, p<0.005). No significant difference in the frequency of codon 52 and 57 mutations was observed between patient and control groups.Conclusions: Mannose binding lectin may be one of the factors that influence the course of HCV infection. Our results suggest that heterozygous carriage of the variant allele of codon 54 of mannose binding lectin is associated with hepatitis C virus infection in our cases. This may not be true about codons 52 and 57 mutations.
Association of STAT4 Polymorphisms with Susceptibility to Type-1 Autoimmune Hepatitis in the Japanese Population  [PDF]
Kiyoshi Migita, Minoru Nakamura, Seigo Abiru, Yuka Jiuchi, Shinya Nagaoka, Atsumasa Komori, Satoru Hashimoto, Shigemune Bekki, Kazumi Yamasaki, Tatsuji Komatsu, Masaaki Shimada, Hiroshi Kouno, Taizo Hijioka, Motoyuki Kohjima, Makoto Nakamuta, Michio Kato, Kaname Yoshizawa, Hajime Ohta, Yoko Nakamura, Eiichi Takezaki, Hideo Nishimura, Takeaki Sato, Keisuke Ario, Noboru Hirashima, Yukio Oohara, Atsushi Naganuma, Toyokichi Muro, Hironori Sakai, Eiji Mita, Kazuhiro Sugi, Haruhiro Yamashita, Fujio Makita, Hiroshi Yatsuhashi, Hiromi Ishibashi, Michio Yasunami
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0071382
Abstract: Background/Aims Recent studies demonstrated an association of STAT4 polymorphisms with autoimmune diseases including systemic lupus erythematosus and rheumatoid arthritis, indicating multiple autoimmune diseases share common susceptibility genes. We therefore investigated the influence of STAT4 polymorphisms on the susceptibility and phenotype of type-1 autoimmune hepatitis in a Japanese National Hospital Organization (NHO) AIH multicenter cohort study. Methodology/Principal Findings Genomic DNA from 460 individuals of Japanese origin including 230 patients with type-1 autoimmune hepatitis and 230 healthy controls was analyzed for two single nucleotide polymorphisms in the STAT4 gene (rs7574865, rs7582694). The STAT4 rs7574865T allele conferred risk for type-1 autoimmune hepatitis (OR = 1.61, 95% CI = 1.23–2.11; P = 0.001), and patients without accompanying autoimmune diseases exhibited an association with the rs7574865T allele (OR = 1.50, 95%CI = 1.13–1.99; P = 0.005). Detailed genotype-phenotype analysis of type-1 autoimmune hepatitis patients with (n = 44) or without liver cirrhosis (n = 186) demonstrated that rs7574865 was not associated with the development of liver cirrhosis and phenotype (biochemical data and the presence of auto-antibodies). Conclusions/Significance This is the first study to show a positive association between a STAT4 polymorphism and type-1 autoimmune hepatitis, suggesting that autoimmune hepatitis shares a gene commonly associated with risk for other autoimmune diseases.
TGF-beta1 Gene Polymorphism in Association with Diabetic Retinopathy Susceptibility: A Systematic Review and Meta-Analysis  [PDF]
Lei Liu, Jinghua Jiao, Yu Wang, Jingyang Wu, Desheng Huang, Weiping Teng, Lei Chen
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0094160
Abstract: Background Transforming growth factor-beta (TGF-β1) gene has been regarded as an important mechanism in angiogenesis, endothelial cell proliferation, adhesion,and the deposition of extracellular matrix. The TGF-β1 gene may be involved in the development of diabetic retinopathy (DR) through disrupting angiogenesis. However, studies investigating the relationship between ?509C/T and +869T/C(L10P) polymorphisms and DR yielded contradictory and inconclusive outcomes. In order to realize these ambiguous findings, a meta-analysis was performed to assess the association between the TGF-β1 gene polymorphisms and susceptibility to DR. Methodology/Principal Findings We conducted a search of all English reports on studies for the association between the TGF-β1 gene polymorphisms and susceptibility to DR using Medline, the Cochrane Library, EMbase, Web of Science, Google (scholar), and all Chinese reports were identified manually and on-line using CBMDisc, Chongqing VIP database, and CNKI database. The strict selection criteria and exclusion criteria were determined, and odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of associations. The fixed or random effect model was selected based on the heterogeneity test among studies. Publication bias was estimated using Begg's funnel plots and Egger's regression test. Results A total of three studies were included in the meta-analysis and all included studies analyzed patients with type 2 diabetes. For +869T/C(L10P) polymorphism, significant association was observed in an allele model (L versus P: OR = 1.34, 95%CI = 1.03–1.73) and the recessive model (LL versus LP+PP: OR = 1.70, 95%CI = 1.13–2.56). As regards ?509C/T polymorphism, no obvious associations were found for all genetic models. Conclusions This meta-analysis suggested that the +869T/C(L10P) polymorphism in TGFβ1 gene would be a potential protect factor for DR. However, the ?509C/T polymorphism is not associated with DR.
Lack of association between the CALM1 core promoter polymorphism (-16C/T) and susceptibility to knee osteoarthritis in a Chinese Han population
Dongquan Shi, Haijian Ni, Jin Dai, Jianghui Qin, Yong Xu, Lunqing Zhu, Chen Yao, Zhenxing Shao, Dongyang Chen, Zhihong Xu, Long Yi, Shiro Ikegawa, Qing Jiang
BMC Medical Genetics , 2008, DOI: 10.1186/1471-2350-9-91
Abstract: A case-control association study was conducted. The polymorphism was genotyped in 183 patients who had primary symptomatic knee OA with radiographic confirmation and in 210 matched controls. Allelic and genotypic frequencies were compared between patients and control subjects.No significant difference was detected in genotype or allele distribution between knee OA and control groups (all P > 0.05). The association was also negative even after stratification by sex. Furthermore, no association between the -16C/T SNP genotype and the clinical variables age, sex, BMI (body mass index) and K/L (Kellgren/Lawrence) score was observed in OA patients.The present study suggests that the CALM1 core promoter polymorphism -16C/T is not a risk factor for knee OA susceptibility in the Chinese Han population. Further studies are needed to give a global view of this polymorphism in pathogenesis of OA.Osteoarthritis (OA) is a common musculoskeletal disease among the elderly, characterized by the degradation of articular cartilage and formation of abnormal bone (osteophyte). It is a multifactorial disorder in which aging, genetic, hormonal and mechanical factors are all major contributors to its onset and progression [1]. Results of family-based and candidate gene studies have demonstrated a clear genetic component, particularly for early-onset OA [2-4]. The identification of candidate genes for OA susceptibility has mainly focused on genes encoding collagens (particularly for type II collagen), for other structural proteins of the extracellular cartilage matrix(ECM), the vitamin D and estrogen receptor genes, and for bone and cartilage growth factors [5]. And it is expected that some genes which regulate the formation, degradation, and repair of articular cartilage and subchondral bone metabolism may determine the occurrence of osteoarthritis. However, the specific underlying genetic factors and mechanisms in the development of osteoarthritis need to be further researched.Calmodulin
Association of XbaI GLUT1 Polymorphism with Susceptibility to Type 2 Diabetes Mellitus and Diabetic Nephropathy  [PDF]
Ragaa Abdelkader Ramadan, Ahmad Mohamed Zaki, Gehan Mahmoud Magour, Moyassar Ahmad Zaki, Sarah Ahmed Aglan, Marwa Ahmed Madkour, Mohammed Mohammed Shamseya
American Journal of Molecular Biology (AJMB) , 2016, DOI: 10.4236/ajmb.2016.62008
Abstract: Objectives: Diabetic nephropathy (DN) is one of the chronic microangiopathic complications of type 2 diabetes (T2DM) and has become the most frequent cause of end-stage renal disease. The XbaI polymorphism in the glucose transporter (GLUT1) has been suggested in the development of DN. We examined the association between XbaI polymorphism of GLUT1 and susceptibility to T2DM and development of DN. Methods: The study included 227 T2DM patients divided into 107 without DN (DM ? DN) and 120 with DN (DM + DN), in addition to 100 apparently healthy controls. Genotyping was done by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). Results: The GLUT1 XbaI T allele was associated with increased susceptibility to T2DM, when comparing the healthy controls to the whole diabetic group, odds ratio (OR) = 1.899, 95% confidence interval (CI) (1.149 - 3.136), p = 0.011. This association was also significant between healthy controls and DM ? DN OR = 1.997 (1.079 - 3.699), p = 0.026 as well as between healthy controls and DM + DN OR = 1.818 (1.016 - 3.253), p = 0.042. However there was no significant association of XbaI polymorphism with DN when comparing DM ? DN to DM + DN OR = 0.910 (0.474 - 1.747), p = 0.777. Conclusion: XbaI T allele is associated with increased susceptibility to T2DM, but not to development of DN. Further studies are needed to replicate such findings.
Population Genetics of GYPB and Association Study between GYPB*S/s Polymorphism and Susceptibility to P. falciparum Infection in the Brazilian Amazon  [PDF]
Eduardo Tarazona-Santos,Lilian Castilho,Daphne R. T. Amaral,Daiane C. Costa,Natália G. Furlani,Luciana W. Zuccherato,Moara Machado,Marion E. Reid,Mariano G. Zalis,Andréa R. Rossit,Sidney E. B. Santos,Ricardo L. Machado,Sara Lustigman
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0016123
Abstract: Merozoites of Plasmodium falciparum invade through several pathways using different RBC receptors. Field isolates appear to use a greater variability of these receptors than laboratory isolates. Brazilian field isolates were shown to mostly utilize glycophorin A-independent invasion pathways via glycophorin B (GPB) and/or other receptors. The Brazilian population exhibits extensive polymorphism in blood group antigens, however, no studies have been done to relate the prevalence of the antigens that function as receptors for P. falciparum and the ability of the parasite to invade. Our study aimed to establish whether variation in the GYPB*S/s alleles influences susceptibility to infection with P. falciparum in the admixed population of Brazil.
Association between low molecular polypeptide 7 single nucleotide polymorphism and response to therapy in hepatitis C virus infection  [cached]
Moataza H Omran,Basma E Fotouh,Samar S Youssef,Noha E Ibrahim
World Journal of Hepatology , 2013, DOI: 10.4254/wjh.v5.i3.97
Abstract: AIM: To investigate the relationship between low molecular polypeptide-7 (LMP-7) gene polymorphism and response to interferon (IFN) therapy in chronic hepatitis C virus (HCV) patients. METHODS: LMP-7 polymorphism at codon 49 with nucleotide substitution from A to C was amplified in 104 chronic HCV patients of genotype 4. The amplicons were digested with restriction endonuclease BsmI and the produced restriction fragment length polymorphism was analyzed. Patients received IFN + regional blood volume therapy for 48 wk and the frequency of this single nucleotide polymorphism (SNP) was statistically correlated with treatment response. The exclusion criteria for these patients were stated by the national health program for treating viral hepatitis. Main exclusion criteria included co-infection with hepatitis B virus or schistosomiasis, thyroid dysfunction, uncontrolled diabetes mellitus, history of long term drug or alcohol intake and autoimmune hepatitis. Multivariate analyses were done to correlate LMP-7 SNP plus several factors such as age, gender, weight, serum alpha-fetoprotein (AFP) and alanine aminotransferase levels, liver activity, fibrosis score and viral load with response to therapy. RESULTS: The data presented in this study clearly demonstrated statistically significant differences between sustained virological response (SVR) (defined as the absence of HCV RNA levels in the patient’s sera at least 6 mo after discontinuation of treatment) and non-response (NR) (where HCV RNA levels in the patient’s sera never become undetectable for 6 mo during or after treatment). Variables were described as odds ratio with 95%CI. The data were considered significant if P values were ≤ 0.05; highly significant if P < 0.01 and very highly significant if P < 0.001. Current data showed that 91.7% of patients carrying LMP-7 C/C allele were associated with SVR, while the other two genotypes C/A and A/A were associated with NR patients, 83.3% and 64.3% respectively, showing that genotype CC was strongly associated with response to interferon (95%CI: 12.0719-134.6572, P = 0.0001). The majority of parameters recorded in SVR and NR patients included higher values of mean age (P = 0.004), alanine aminotransferase (P = 0.001), AFP (P = 0.001), body weight (P = 0.025), viral load (P = 0.025), higher fibrosis and histological activity index indices among NR vs SVR patients. Also, the multivariate statistical analysis of the different factors of fibrosis score, liver activity grade, genotypes and alleles of LMP-7 gene polymorphism in responders and NRs of HCV patients in this
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