Tetra Amplification Refractory Mutation System-polymerase Chain Reaction Research Articles

Investigation of CTLA‐4 and CD86 gene polymorphisms in Iranian patients with brucellosis infection

The protective immune response against Brucella involves T-cell-mediated immunity. T-lymphocyte receptors, CD28 and cytotoxic T-lymphocyte-associated protein-4 (CTLA-4), bind the same ligands, CD80 (B7-1) and CD86 (B7-2) on antigen-presenting cells and regulate T cell activation. CD28 delivers stimulatory signals whereas CTLA-4 provides inhibitory signals for T cell activation. Here, we investigated the association of four polymorphisms in CTLA4 (+49A/G [rs231775] and -318 C/T [rs5742909]) and its ligand CD86 (+1057 G/A [rs1129055] and +2379G/C [rs17281995]) with brucellosis infection. The study included 153 Iranian patients with active brucellosis and 128 healthy individuals as the control group. Genotyping of the CTLA4 and CD86 variants was performed using tetra amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) and PCR-restriction fragment length polymorphism analysis, respectively. It was found that the CTLA4 -318 CT genotype and T allele were present more frequently in cases than in controls and are therefore associated with an increased risk for brucellosis (-318 TT genotype; OR = 2.544, P = 0.002). Likewise, the CD86 +1057 GA and AA genotypes and A allele were associated with an increased risk of brucellosis (+1057 AA genotype; OR = 3.81, P = 0.001). However, no statistically significant difference between brucellosis patients and controls in the allele and genotype distributions of CTLA4, +49A/G (P = 0.859) and CD86, +2379G/C (P = 0.476) was found. In conclusion, CTLA4 -318 CT genotype and T allele and the CD86 +057 GA and AA genotypes and A allele play roles as risk factors for developing brucellosis infection in Iran.

Investigation of FGF1 and FGFR gene polymorphisms in a group of Iranian patients with nonsyndromic cleft lip with or without cleft palate

ObjectiveNonsyndromic cleft lip with or without cleft palate (NS-CL/P) is one of the most common craniofacial malformations determined by the interaction between multiple genes and environmental risk factors. Genes coding for fibroblast growth factors and their receptors (FGF/FGFR genes) are considered as excellent candidate genes, which their proteins play important roles in craniofacial and palatal development. The aim of the current study was to assess the possible association between FGF1 rs34010 C>A and FGFR1 rs13317 A>G gene polymorphisms and susceptibility to NS-CL/P in an Iranian population. DesignThis case–control retrospective study was performed on a total of 200 subjects including 100 NS-CL/P patients and 100 healthy unrelated controls. Tetra amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) was used to detect FGF1 rs34010 C>A and FGFR1 rs13317 A>G SNPs. ResultsOur data demonstrated that the FGF1 rs34010, CA and CA+AA genotypes were associated with a reduced risk of NS-CL/P the in codominant (CA vs. CC: OR=0.29, 95%CI=0.16–0.55, P=0.001) and dominant (CA+AA vs. CC: OR=0.36, 95%CI=0.19–0.69, P=0.001) tested inheritance models, respectively. Additionally, the analysis of FGF1/FGFR1 genotype combinations revealed that rs34010CA/rs13317AA and rs34010CA/rs13317AG combinations were associated with a lower risk of NS-CL/P (OR=0.357, P=0.008 for the rs34010CA/rs13317AA; OR=0.226, P=0.004 for the rs34010CA/rs13317AG). ConclusionsOur findings suggest that the FGF1 rs34010 C/A polymorphism was associated with a decreased risk of NS-CL/P, and might act as a protective factor against NS-CL/P predisposition.

Association between toll-like receptor2 Arg677Trp and 597T/C gene polymorphisms and pulmonary tuberculosis in Zahedan, Southeast Iran

BackgroundIt is well known that toll-like receptor 2 (TLR2) mediates responses of both innate and adaptive immunity to microbial pathogen, including mycobacteria. Single-nucleotide polymorphisms (SNPs) in the TLR2 gene that impair its function may be associated with the development of pulmonary tuberculosis (PTB). The aim of this study was to evaluate the possible association between TLR2 Arg677Trp and 597T/C polymorphisms and PTB in a sample of Iranian population. Materials and methodsThis case–control study was performed on 174 PTB and 177 healthy subjects. Tetra amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) was used to detect the SNPs. ResultsThere was no significant difference in the polymorphism of Arg677Trp of the TLR2 gene among PTB and control groups (p>0.05). The results showed that there was a significant difference between case and control groups regarding 597T/C polymorphism (χ2=12.21, p=0.002). The TC and CC genotypes were found to be associated with the risk of PTB (OR=2.13, 95% CI=1.25–3.62, p=0.005 and OR=4.88, 95% CI=1.56–15.26, p=0.007, respectively). ConclusionOur data suggest that 597T/C polymorphism, but not Arg677Trp polymorphism, of the TLR-2 gene is a risk factor for susceptibility to PTB in a sample of Iranian population.

Associação entre o polimorfismo rs7700944 no gene TIM-4 e artrite reumatoide em Zahedan, sudeste do Irã

IntroductionRecently, an association between rheumatoid arthritis (RA) and the rs7700944 G>A variant in the T-cell immunoglobulin and mucin domains 4 (TIM-4) has been reported. ObjectiveThe present study aimed at investigating the impact of that polymorphism on susceptibility to RA in a sample of the Iranian population. Patients and methodsThis case-control study was conducted on 120 patients with RA and 120 healthy subjects. The rs7700944 polymorphism in the TIM-4 gene was determined using tetra amplification refractory mutation system-polymerase chain reaction (T-ARMSPCR) assay. ResultsNo significant difference was observed regarding the rs7700944 polymorphism of the TIM-4 gene between patients with RA and normal individuals. In females, no significant association was found between the groups concerning the rs7700944 polymorphism of the TIM-4 gene. In males, the GA+AA genotype increased the risk of RA in comparison with the GG genotype (OR=5.15, 95% CI=1.30-20.48, P=0.020). Furthermore the results showed that the rs7700944 A allele increased the risk of RA (OR=4.39, 95% CI=1.43-13.54, P=0.009). ConclusionOur results do not support an association between the rs7700944 polymorphism of the TIM-4 gene and RA. An interaction between this polymorphism and sex suggests a sex-specific association between this single nucleotide polymorphism and RA, which remains to be fully elucidated.

Association between the rs7700944 polymorphism in the TIM-4 gene and rheumatoid arthritis in Zahedan, southeast Iran

IntroductionRecently, an association between rheumatoid arthritis (RA) and the rs7700944 G>A variant in the T-cell immunoglobulin and mucin domains 4 (TIM-4) has been reported. ObjectiveThe present study aimed at investigating the impact of that polymorphism on susceptibility to RA in a sample of the Iranian population. Patients and methodsThis case-control study was conducted on 120 patients with RA and 120 healthy subjects. The rs7700944 polymorphism in the TIM-4 gene was determined using tetra amplification refractory mutation system-polymerase chain reaction (T-ARMSPCR) assay. ResultsNo significant difference was observed regarding the rs7700944 polymorphism of the TIM-4 gene between patients with RA and normal individuals. In females, no significant association was found between the groups concerning the rs7700944 polymorphism of the TIM-4 gene. In males, the GA+AA genotype increased the risk of RA in comparison with the GG genotype (OR=5.15, 95% CI=1.30-20.48, P=0.020). Furthermore the results showed that the rs7700944 A allele increased the risk of RA (OR=4.39, 95% CI=1.43-13.54, P=0.009). ConclusionOur results do not support an association between the rs7700944 polymorphism of the TIM-4 gene and RA. An interaction between this polymorphism and sex suggests a sex-specific association between this single nucleotide polymorphism and RA, which remains to be fully elucidated.

Association of PTPN22 rs2476601 and EGFR rs17337023 Gene polymorphisms and rheumatoid arthritis in Zahedan, Southeast Iran

In this study we aimed to evaluate the possible association of PTPN22 rs2476601 as well as epidermal growth factor receptor (EGFR) rs17337023 gene polymorphism and rheumatoid arthritis (RA) in a sample of Iranian population. This case-control study was performed on 120 patients with RA and 120 healthy subjects. Genomic DNA was extracted from whole blood and PTPN22 rs2476601 and EGFR rs17337023 polymorphisms were determined using tetra amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR). The results showed that PTPN22 rs2476601 CT genotype as well as rs2476601 T allele was a risk factor for susceptibility to RA (OR=5.89 95%CI = 1.78-19.48, P = 0.004 and OR = 4.78, 95%CI = 1.59-14.35, P = 0.003, respectively). We also found that EGFR rs17337023 AT and rs17337023 TT genotypes were risk factor for susceptibility to RA (OR = 9.94 95%CI = 3.65-26.73, P < 0.001 and OR = 3.66, 95%CI = 1.46-9.15, P = 0.005, respectively). In addition the EGFR rs17337023 T allele was a risk for predisposition to RA (OR = 1.56, 95%CI=1.06-2.30, P = 0.030). In conclusion, we found an association between PTPN22 rs2476601 and EGFR rs17337023 polymorphisms and the risk of RA in a sample of Iranian population.

Association of TGF-β1 − 509 C/T, 29 C/T and 788 C/T gene polymorphisms with chronic periodontitis: A case–control study

The aim of this study was to investigate the possible association between TGF-β1 −509 C/T (rs1800469), 29 C/T (Prol10Leu, rs1800470) and 788 C/T (Thr263Ile, rs1800472) gene polymorphisms and chronic periodontitis (CP) in a sample of Iranian population. This case–control study was conducted on 100 CP patients and 100 healthy unrelated, age-, sex-, and ethnicity-matched. Genotyping was performed by tetra amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) technique. Our findings showed that there was a significant difference between the groups regarding TGF-β1 29 C/T (rs1800470) polymorphism (χ2=23.23, P<0.0001). The CT and TT genotypes increased the risk of CP in comparison with the CC genotype (OR=4.42, 95% CI=2.16–9.06, P<0.001 and OR=5.84, 95% CI=2.32–14.71, P<0.001, respectively). The T allele increased the risk of CP (OR=2.50, 95% CI=1.66–3.74, P<0.001) in comparison with C allele. No significant association was found among the groups regarding −509 C/T and 788 C/T variants of TGF-β1 gene. This study shows that TGF-β1 29 C/T polymorphism, but not −509 C/T and 788 C/T polymorphisms, may contribute to the development of CP in a sample of Iranian population. Further studies with larger sample sizes and different ethnicities are needed to validate our findings.

Association Between Betaine Homocysteine S-Methyl Transferase (BHMT) rs3797546 Gene Polymorphisms and the Risk of Nonsyndromic Cleft Lip and/or Cleft Palate in South-East Population of Iran

Background: Nonsyndromic cleft lip with or without cleft palate (NS-CL/P) is one of the most common congenital anomalies and has a multifactorial etiology that involves both genetic and environmental factors. Objectives: The present study was aimed to evaluate the possible association between BHMT rs3797546 gene polymorphisms and NS-CL/P in a sample of Iranian population. Materials and Methods: This case-control study was performed on 100 NS-CL/P cases and 100 healthy controls. Tetra amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) was used to detect the polymorphism. Analysis of data was done using χ2 test for categorical data, the associations between genotypes and NS-CL/P were estimated by computing the odds ratio (OR) and 95% confidence intervals (95% CI) from logistic regression analyses. Results: No significant difference was found between the groups regarding BMHT rs3797546 gene polymorphism. The C allele was not associated with NS-CL/P (OR = 1.27, 95% CI = 0.85-2.79, P = 0.690). Conclusions: Our data suggested that BMHT rs3797546 gene polymorphism was not associated with risk/ protection for NS-CL/P in a sample of Iranian population. Larger studies are required to validate our findings.

Association between chemerin rs17173608 and vaspin rs2236242 gene polymorphisms and the metabolic syndrome, a preliminary report

Metabolic syndrome (MeS) is associated with increased risk for type 2 diabetes mellitus (T2DM) and cardiovascular disease. There is some evidence indicating that adipokines play a role in the development of MeS. The present study was aimed to investigate the impact of chemerin rs17173608 and vaspin rs2236242 gene polymorphisms with the risk of MeS in a sample of Iranian population.This case‐control study was done on 151 subjects with MeS and 149 without MeS, as defined by NCEP-ATPIII. Tetra amplification refractory mutation system‐polymerase chain reaction (T-ARMS-PCR) was designed to detect the polymorphisms. Our finding showed that there are significant differences in genotype frequencies between the groups regarding vaspin rs2236242 polymorphism (χ2=18.74, p<0.0001). A significant protection against MeS was found for vaspin rs2236242 in allele and genotypes (Odd Ratio [OR]=0.52; 95% confidence interval [CI]=0.37–0.72; p=0.0001, T vs A; OR=0.49; 95%CI=0.29–0.82; p=0.007, TT vs TA and OR=0.17; 95%CI=0.07–0.40; p<0.0001, TT vs AA). Our finding showed positive association between chemerin rs17173608 polymorphism and risk of MeS (χ2=7.70, p=0.021). The G allele increased the risk of MeS (OR=1.78; 95% CI=1.14-2.78; p=0.012) as compared to the T allele. In conclusion, our data suggest for the first time a significant association between vaspin rs2236242 and chemerin rs17173608 polymorphisms and the MeS in Zahedan, southeast Iran. Further studies with large sample size and different ethnicities are required to confirm our findings.