Association of Polymorphisms in Glutamate-Cysteine Ligase Catalytic Subunit and Microsomal Triglyceride Transfer Protein Genes with Nonalcoholic Fatty Liver Disease

Oxidative Stress in Non-Alcoholic Fatty Liver Disease

Non-alcoholic fatty liver disease (NAFLD) is a challenging disease caused by multiple factors, which may partly explain why it still remains an orphan of adequate therapies. This review highlights the interaction between oxidative stress (OS) and disturbed lipid metabolism. Several reactive oxygen species generators, including those produced in the gastrointestinal tract, contribute to the lipotoxic hepatic (and extrahepatic) damage by fatty acids and a great variety of their biologically active metabolites in a “multiple parallel-hit model”. This leads to inflammation and fibrogenesis and contributes to NAFLD progression. The alterations of the oxidant/antioxidant balance affect also metabolism-related organelles, leading to lipid peroxidation, mitochondrial dysfunction, and endoplasmic reticulum stress. This OS-induced damage is at least partially counteracted by the physiological antioxidant response. Therefore, modulation of this defense system emerges as an interesting target to prevent NAFLD development and progression. For instance, probiotics, prebiotics, diet, and fecal microbiota transplantation represent new therapeutic approaches targeting the gut microbiota dysbiosis. The OS and its counter-regulation are under the influence of individual genetic and epigenetic factors as well. In the near future, precision medicine taking into consideration genetic or environmental epigenetic risk factors, coupled with new OS biomarkers, will likely assist in noninvasive diagnosis and monitoring of NAFLD progression and in further personalizing treatments.

Effect of MTTP -493G/T, I128T, Q95H and Q244E polymorphisms on hepatic steatosis in patients with chronic hepatitis

BACKGROUND

Chronic hepatitis C is characterized by a progressive deterioration of liver function and is involved in metabolic complications, such as hepatic steatosis.

OBJECTIVE

The aim of this study was to investigate the role of host and viral characteristics associated with -493G/T (rs1800591), I128T (rs3816873), Q95H (rs61733139), and Q244E (rs17599091) Single Nucleotide Polymorphisms (SNPs) in the Microsomal Triglyceride Transfer Protein (MTTP) gene on hepatic steatosis in chronic hepatitis C.

METHODS

SNPs were genotyped by PCR-RFLP and analyzed in combination with host and viral characteristics by multiple logistic regression in different genetic models of inheritance.

RESULTS

The authors analyzed 236 patients with chronic hepatitis C, and 53% had hepatic steatosis. The mutated allele frequencies were > 5%, and the genotypes were in Hardy-Weinberg equilibrium (p ≥ 0.05). It was observed that patients with HCV genotype 3 infection (OR = 2.74, 95% CI 1.24‒6.06, p = 0.013), female sex (OR = 2.28, 95% CI 1.21‒4.28, p = 0.011) and moderate- and high-intensity liver inflammatory activity (A2-A3) (OR = 3.61, 95% CI 1.86‒7.01, p < 0.001) alone exhibited a higher risk of steatosis. The results of multiple logistic regression analysis for interaction showed that for the -493G/T SNP, when the GT/TT genotype (dominant model) and the GT genotype (codominant model) were each combined with HCV genotype 3 infection, an 11.51-fold (95% CI 2.08‒63.59, p = 0.005) and a 15.69-fold (95% CI 2.46‒99.85, p = 0.004) increased risk of steatosis, respectively, was observed. For the I128T SNP, when both the IT/TT genotype (dominant model) and the IT genotype (codominant model) were combined with HCV genotype 3 infection, an 8.51-fold (95% CI 1.59‒45.54, p = 0.012) and an 8.40 fold (95% CI 1.51‒46.91, p = 0.015) increased risk of steatosis, respectively, was observed.

CONCLUSION

The present study showed that the viral genotype combined with the -493G/T and I128T SNPs in the MTTP gene influences hepatic steatosis.

Genome-wide association analysis of serum alanine and aspartate aminotransferase, and the modifying effects of BMI in 388k European individuals

Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) are biomarkers for liver health. Here we report the largest genome-wide association analysis to date of serum ALT and AST levels in over 388k people of European ancestry from UK biobank and DiscovEHR. Eleven million imputed markers with a minor allele frequency (MAF) ≥ 0.5% were analyzed. Overall, 300 ALT and 336 AST independent genome-wide significant associations were identified. Among them, 81 ALT and 61 AST associations are reported for the first time. Genome-wide interaction study identified 9 ALT and 12 AST independent associations significantly modified by body mass index (BMI), including several previously reported potential liver disease therapeutic targets, for example, PNPLA3, HSD17B13, and MARC1. While further work is necessary to understand the effect of ALT and AST-associated variants on liver disease, the weighted burden of significant BMI-modified signals is significantly associated with liver disease outcomes. In summary, this study identifies genetic associations which offer an important step forward in understanding the genetic architecture of serum ALT and AST levels. Significant interactions between BMI and genetic loci not only highlight the important role of adiposity in liver damage but also shed light on the genetic etiology of liver disease in obese individuals.

Spinach consumption and nonalcoholic fatty liver disease among adults: a case-control study

BACKGROUND

Spinach has high antioxidants and polyphenols and showed protective effects against liver diseases in experimental studies. We aimed to assess the association between dietary intake of spinach and odds of nonalcoholic fatty liver disease (NAFLD) in a case-control study among Iranian adults.

METHODS

Totally 225 newly diagnosed NAFLD patients and 450 controls, aged 20-60 years, were recruited in this study. Participants' dietary intakes were collected using a valid and reliable 168-item semi-quantitative food frequency questionnaire (FFQ). The logistic regression test was used for assessing the association between total, raw, and boiled dietary spinach with the odds of NAFLD.

RESULTS

The mean (SD) age and BMI of participants (53% male) were 38.1 (8.8) years and 26.8 (4.3) kg/m², respectively. In the final adjusted model for potential confounders, the odds (95% CI) of NAFLD in individuals in the highest tertile of daily total and raw spinach intake was [0.36 (0.19-0.71), P_trend = 0.001] and [0.47 (0.24-0.89), P_trend = 0.008], respectively compared with those in the lowest tertile. Furthermore, in the adjusted analyses, an inverse association was observed between the highest yearly intake versus no raw spinach consumption and odds of NAFLD [(OR 0.41; 95% CI 0.18-0.96), P for trend = 0.013]. However, there was no significant association between higher boiled spinach intake and odds of NAFLD.

CONCLUSIONS

The present study found an inverse association between total and raw spinach intake with the odds of NAFLD.

Deciphering the Variants Located in the MIR196A2, MIR146A, and MIR423 with Type-2 Diabetes Mellitus in Pakistani Population

MicroRNAs (miRNAs) are small non-coding RNA molecules that control the post-transcriptional gene expression. They play a pivotal role in the regulation of important physiological processes. Variations in miRNA genes coding for mature miRNA sequences have been implicated in several diseases. However, the association of variants in miRNAs genes with Type 2 Diabetes Mellitus (T2DM) in the Pakistani population is rarely reported. Therefore, the current study was designed to investigate the association of rs11614913 T/C (MIR196A2), rs2910164 G/C (MIR146A), and rs6505162 C/A (MIR423) in clinicopathological proven T2DM patients and gender-matched healthy controls. The tetra-primer amplification refractory mutation system-polymerase chain (ARMS-PCR) reaction method was used to determine the genotypes and to establish the association of each variant with T2DM through inherited models. In conclusion, the present study showed that variants rs11614913 T/C and rs2910164 G/C were linked with the risk of T2DM. The data suggested that rs11614913 T/C and rs2910164 G/C could be considered as novel risk factors in the pathogenesis of T2DM in the Pakistani population.

The association between SNPs rs1800591 and rs3816873 of the MTTP gene and nonalcoholic fatty liver disease: A meta-analysis

BACKGROUND/AIMS

: The role of two polymorphisms rs1800591 and rs3816873 of the microsomal triglyceride transfer protein (MTTP) gene in the development of nonalcoholic fatty liver disease (NAFLD) remains controversial. A meta-analysis was conducted to determine the correlation between these MTTP polymorphisms and NAFLD.

MATERIALS AND METHODS

: A systematic search was carried out using PubMed, Embase, and Cochrane Library to retrieve English studies that reported the relationship between MTTP polymorphisms (rs1800591 and rs3816873) and NAFLD published before February 18, 2020. Odds ratio (OR) and 95% confidence interval (CI) were used to appraise the risk of MTTP polymorphism in NAFLD.

RESULTS

: A total of 10 case-control studies, including 1388 cases and 1690 healthy subjects, were included. No significant correlation between the rs1800591 (G vs. T: OR = 1.08, 95% CI = 0.68-1.70, P = 0.76) and rs3816873 (CT + CC vs. TT: OR = 1.23, 95% CI = 0.76-2.01, P = 0.398) polymorphisms of MTTP and NAFLD was found in any of the models. However, when NASH patients confirmed by liver biopsy were extracted alone for rs1800591 polymorphism analysis, it was found that the G allele significantly increased the risk of NASH under the heterozygote model (GT vs. TT: OR = 3.16, 95% CI = 1.13-8.83, P = 0.028) and dominant model (GT + GG vs. TT: OR = 3.03, 95% CI = 1.13-8.09, P = 0.027).

CONCLUSION

The present meta-analysis revealed that the rs1800591 and rs3816873 polymorphisms of the MTTP gene are uncommon in NAFLD. However, the G allele of rs1800591 was more likely to be correlated to NASH susceptibility.

Oxidative Stress and Non-Alcoholic Fatty Liver Disease: Effects of Omega-3 Fatty Acid Supplementation

Aging is a complex phenomenon characterized by the progressive loss of tissue and organ function. The oxidative-stress theory of aging postulates that age-associated functional losses are due to the accumulation of ROS-induced damage. Liver function impairment and non-alcoholic fatty liver disease (NAFLD) are common among the elderly. NAFLD can progress to non-alcoholic steatohepatitis (NASH) and evolve to hepatic cirrhosis or hepatic carcinoma. Oxidative stress, lipotoxicity, and inflammation play a key role in the progression of NAFLD. A growing body of evidence supports the therapeutic potential of omega-3 polyunsaturated fatty acids (n-3 PUFA), mainly docosahaexenoic (DHA) and eicosapentaenoic acid (EPA), on metabolic diseases based on their antioxidant and anti-inflammatory properties. Here, we performed a systematic review of clinical trials analyzing the efficacy of n-3 PUFA on both systemic oxidative stress and on NAFLD/NASH features in adults. As a matter of fact, it remains controversial whether n-3 PUFA are effective to counteract oxidative stress. On the other hand, data suggest that n-3 PUFA supplementation may be effective in the early stages of NAFLD, but not in patients with more severe NAFLD or NASH. Future perspectives and relevant aspects that should be considered when planning new randomized controlled trials are also discussed.

Development of gene polymorphisms in meditators of nonalcoholic fatty liver disease

Nonalcoholic fatty liver disease (NAFLD) is the most prevalent liver disease worldwide, the morbidity of which closely correlates with diversity of ethnicity, minority, family and location. Its histology spans from simple steatosis, to nonalcoholic steatohepatitis, which ultimately results in fibrosis, cirrhosis and hepatocellular carcinoma. The accelerating prevalence of NAFLD is due to an incremental incidence of metabolic syndrome that is distinguished by dyslipidemia, glucose impairment, obesity, excessive oxidative stress and adipocytokine impairment. Additionally, the pathogenesis of NAFLD is thought to be a multifactorial and complicated disease associated with lifestyle habits, nutritional factors and genetics. However, the pathogenesis and underlying mechanism in the development of NAFLD caused by genetics remains unclear. People have been increasingly emphasizing on the relationship between NAFLD and gene polymorphisms in recent years, with the aim of having a comprehensive elucidation of associated gene polymorphisms influencing the pathogenesis of the disease. In the current article, the authors attempted to critically summarize the most recently identified gene polymorphisms from the facets of glucose metabolism, fatty acid metabolism, oxidative stress and related cytokines in NAFLD that contribute to promoting the progression of the disease.

Gclc deficiency in mouse CNS causes mitochondrial damage and neurodegeneration

Gamma glutamyl cysteine ligase (GCL) is the rate-limiting enzyme for intracellular glutathione (GSH) synthesis. The GSH concentration and GCL activity are declining with age in the central nervous system (CNS), and is accompanied by elevated reactive oxygen species (ROS). To study the biological effects of low GSH levels, we disrupted its synthesis both at birth by breeding a Gclc loxP mouse with a thy1-cre mouse (NEGSKO mouse) and at a later age by breeding with a CaMKII-ERT2-Cre (FIGSKO mouse). NEGSKO mice with deficiency of the Gclc in their entire CNS neuronal cells develop at 4 weeks: progressive motor neuron loss, gait problems, muscle denervation and atrophy, paralysis, and have diminished life expectancy. The observed neurodegeneration in Gclc deficiency is of more chronic rather than acute nature as demonstrated by Gclc targeted single-neuron labeling from the inducible Cre-mediated knockout (SLICK) mice. FIGSKO mice with inducible Gclc deficiency in the forebrain at 23 weeks after tamoxifen induction demonstrate profound brain atrophy, elevated astrogliosis and neurodegeneration, particularly in the hippocampus region. FIGSKO mice also develop cognitive abnormalities, i.e. learning impairment and nesting behaviors based on passive avoidance, T-Maze, and nesting behavior tests. Mechanistic studies show that impaired mitochondrial glutathione homeostasis and subsequent mitochondrial dysfunction are responsible for neuronal cell loss. This was confirmed by mitochondrial electron transporter chain activity analysis and transmission electron microscopy that demonstrate remarkable impairment of state 3 respiratory activity, impaired complex IV function, and mitochondrial swollen morphology in the hippocampus and cerebral cortex. These mouse genetic tools of oxidative stress open new insights into potential pharmacological control of apoptotic signaling pathways triggered by mitochondrial dysfunction.

Gestational exercise protects adult male offspring from high-fat diet-induced hepatic steatosis

BACKGROUND & AIMS

Mounting evidence indicates that maternal exercise confers protection to adult offspring against various diseases. Here we hypothesized that maternal exercise during gestation would reduce high-fat diet (HFD)-induced hepatic steatosis in adult rat offspring.

METHODS

Following conception, pregnant dams were divided into either voluntary wheel running exercise (GE) or wheel-locked sedentary (GS) groups throughout gestation (days 4-21). Post-weaning, offspring received either normal chow diet (CD; 10% fat, 70% carbohydrate, 20% protein) or HFD (45% fat, 35% carbohydrate, and 20% protein) until sacrificed at 4- or 8-months of age.

RESULTS

GE did not affect offspring birth weight or litter size. HFD feeding in offspring increased weight gain, body fat percentage, and glucose tolerance test area under the curve (GTT-AUC). Male offspring from GE dams had reduced body fat percentage across all ages (p<0.05). In addition, 8-month male offspring from GE dams were protected against HFD-induced hepatic steatosis, which was associated with increased markers of hepatic mitochondrial biogenesis (PGC-1α and TFAM), autophagic potential (ATG12:ATG5 conjugation) and hepatic triacylglycerol secretion (MTTP).

CONCLUSIONS

The current study provides the first evidence that gestational exercise can reduce susceptibility to HFD-induced hepatic steatosis in adult male offspring.

Lack of Association between Interleukin-18 –607 C/A Gene Polymorphism and Pulmonary Tuberculosis in Zahedan, Southeast Iran

Interleukin-18 (IL-18) plays a critical role in immune response, contributing to the pathogenesis and pathophysiology of infectious diseases. Polymorphisms in the IL-18 genes are known to influence expression levels and may be associated with outcome of infections. The objective of this study was to determine whether the presence of IL-18 polymorphisms –607 A/C (rs1946518) was associated with tuberculosis disease. We investigated the functional polymorphism of IL-18 (rs1946518) in 174 patients with pulmonary tuberculosis (PTB) and 177 healthy subjects. Genotype analysis was done using tetra amplification refractory mutation system-PCR (T-ARMS-PCR). The allelic and genotypic frequencies of the IL-18 polymorphism did not differ significantly between PTB and the controls. Our finding suggests that IL-18 polymorphism (rs1946518) may not be a risk factor for susceptibility to tuberculosis in a sample of Iranian population. Further studies are required to validate our findings.

Genetic polymorphisms and oxidative stress in non-alcoholic steatohepatitis (NASH): A mini review

Non-alcoholic fatty liver disease (NAFLD) is the most common form of liver disease, thus becoming an epidemic in the Western world with a major impact on public health. NAFLD encompasses a large spectrum of disease ranging from simple steatosis to non-alcoholic steatohepatitis (NASH) and may progress to fibrosis, cirrhosis and hepatocellular carcinoma (HCC). The role of genetic polymorphisms is not clear. Evidence supports the hypothesis that genetic factors are involved in the predisposition to NAFLD, and thus should emphasize the polygenic nature of the disease as a limiting factor in these studies. However, the polymorphic allele associated with increased hepatic steatosis appears to be associated with various different combinations of phenotypes, including increase or decrease of the biochemical and clinical parameters. It is possible that SNPs in genes involved in excessive fatty acid oxidation would predispose to NASH. On the other hand, the SNPs could determine the inadequate mitochondrial overload during times of excessive FFA supply. However due to the multiple hits involving some pathways, a brief review of genetic variants on mediators of oxidative stress, inflammation and lipid metabolism pathways is presented. It is clear that the discovery of genetic and environmental associations, robust enough to direct the treatment and to trace specific prevention strategies would only be possible with studies examining the susceptibility of NAFLD in a number of individuals considerably higher than assessed so far. These studies need a large number of well phenotyped cases and controls and certainly require national and international collaboration.

Genetic analysis of nonalcoholic fatty liver disease within a Caribbean-Hispanic population

We explored potential genetic risk factors implicated in nonalcoholic fatty liver disease (NAFLD) within a Caribbean–Hispanic population in New York City. A total of 316 individuals including 40 subjects with biopsy‐proven NAFLD, 24 ethnically matched non‐NAFLD controls, and a 252 ethnically mixed random sampling of Bronx County, New York were analyzed. Genotype analysis was performed to determine allelic frequencies of 74 known single‐nucleotide polymorphisms (SNPs) associated with NAFLD risk based on previous genome‐wide association study (GWAS) and candidate gene studies. Additionally, the entire coding region of PNPLA3, a gene showing the strongest association to NAFLD was subjected to Sanger sequencing. Results suggest that both rare and common DNA variations in PNPLA3 and SAMM50 may be correlated with NAFLD in this small population study, while common DNA variations in CHUK and ERLIN1, may have a protective interaction. Common SNPs in ENPP1 and ABCC2 have suggestive association with fatty liver, but with less compelling significance. In conclusion, Hispanic patients of Caribbean ancestry may have different interactions with NAFLD genetic modifiers; therefore, further investigation with a larger sample size, into this Caribbean–Hispanic population is warranted.

TIRAP rs8177374 gene polymorphism increased the risk of pulmonary tuberculosis in Zahedan, southeast Iran

OBJECTIVE

To evaluate the possible association between Toll-interleukin 1 receptor (TIR) domain containing adaptor protein (TIRAP; also known as MAL) rs1893352 and rs8177374 (S180L) gene polymorphisms and pulmonary tuberculosis (PTB) in a sample of Iranian population.

METHODS

This 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 polymorphisms.

RESULTS

Our finding showed that neither the overall Chi-square comparison of PTB and control subjects nor the logistic regression analysis indicated any association between rs1893352 polymorphism and PTB. Regarding rs8177374 polymorphism, the CT genotype as well as CT+TT increased the risk of PTB in comparison with CC genotype (OR=4.73, 95% CI=2.65-8.45, P<0.0001 and OR=6.47, 95% CI=3.68-11.38, P<0.0001, respectively). The rs8177374 T allele increased the risk of PTB in comparison with C allele (OR=4.21, 95% CI=2.43-7.26, P<0.0001).

CONCLUSIONS

Our finding indicates that TIRAP rs8177374 polymorphism is associated with PTB in a sample of Iranian population.

hsa-mir-499 rs3746444 gene polymorphism is associated with susceptibility to breast cancer in an Iranian population

AIM

Our study aimed to evaluate the possible association between four miRNA polymorphisms, hsa-miR-146a (rs2910164 G>C), hsa-miR-499 (rs3746444 T>C) and hsa-miRNA-196a2 (rs11614913 C>T and rs185070757 T>G), and susceptibility to breast cancer in an Iranian population.

MATERIALS & METHODS

In this case-control study we enrolled 236 patients with breast cancer and 203 healthy individuals. Tetra primer amplification refractory mutation system PCR was applied for genotyping the four miRNA SNPs.

RESULTS

Our study indicated that the hsa-mir-499 rs3746444 CC homozygote increased the risk of breast cancer in the dominant (odds ratio [OR]: 2.42; 95% CI: 1.43-4.09; p = 0.001; CC vs TT) and recessive (OR: 2.48; 95% CI: 1.49-4.13; p = 0.004; CC vs TT+TC) inheritance models tested. In addition, the rs3746444 C allele increased the risk of breast cancer (OR: 1.71; 95% CI: 1.27-2.29; p = 0.0004) in comparison with the T allele. However, distribution of the rs2910164 G>C, rs11614913 C>T and rs185070757 T>G genotypes was not statistically different between cases and controls (p > 0.05).

CONCLUSION

Our findings demonstrated that the hsa-mir-499 rs3746444 polymorphism is associated with higher risk of developing breast cancer in our population.

A polymorphism in the microsomal triglyceride transfer protein can predict the response to antiviral therapy in Egyptian patients with chronic hepatitis C virus genotype 4 infection

BACKGROUND/AIMS

A polymorphism in the microsomal triglyceride transfer protein (MTP) is associated with hepatic fibrosis, and carriers showed higher levels of steatosis, higher levels of hepatitis C virus (HCV) RNA and advanced fibrosis. The aim of this study was to study MTP expression pattern in HCV patients and impact of the MTP polymorphism on the response to antiviral therapy.

METHODS

One hundred consecutive naive HCV genotype 4 patients were recruited to receive antiviral therapy, and 40 control subjects were also recruited. Demographic, laboratory, and histopathology data were collected. DNA was isolated, and the samples were subjected to polymerase chain reaction analysis and genotyping for MTP by restriction fragment length polymorphism analysis.

RESULTS

Patients and controls were age- and sex-matched (male/female, 56/44, age, 39.2±7.8 years for patients with HCV; male/female, 18/22, age, 38.1±8.1 years for controls). MTP single nucleotide polymorphisms (SNPs) (GG, GT, TT) and alleles (G, T) in the patients versus the controls were 70%, 21%, 9% & 80.5%, 19.5% versus 10%, 87.5%, 2.5% & 53.8%, 46.3%, respectively (p=0.0001). The sustained viral response (SVR) of the patients was 60%. SNPs in MTP genotypes (GG, GT, and TT) and alleles (G and T) in the responders and nonresponders were 71.7%, 25%, 3.3% & 84.2%, 15.8% versus 67.5%, 15%, 17.5% & 75%, 25% (p=0.038 and p=0.109, respectively). A multivariate analysis showed that the GT genotype was an independent predictor of SVR (area under the curve 90% and p=0.0001).

CONCLUSIONS

MTP could be a new predictor for SVR to antiviral therapy in patients with HCV genotype 4 infection.

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

OBJECTIVE

Nonsyndromic 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.

DESIGN

This 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.

RESULTS

Our 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).

CONCLUSIONS

Our 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.

MTP -493G>T polymorphism and susceptibility to nonalcoholic fatty liver disease: a meta-analysis

Microsomal transfer protein (MTP), a lipid transfer protein localized in the endoplasmic reticulum of hepatocytes and enterocytes, plays an important role in the development of nonalcoholic fatty liver disease (NAFLD). Many existing studies have demonstrated that a common polymorphism (-493G>T, rs1800591 G>T) in the MTP gene may be implicated in the development and progression of NAFLD, but individually published results are inconclusive. This meta-analysis aimed to investigate whether MTP -493G>T polymorphism may be a potential risk factor for NAFLD. We searched CISCOM, CINAHL, Web of Science, PubMed, Google Scholar, EBSCO, Cochrane Library, and CBM databases from inception through October 1, 2013. Meta-analysis was performed using the STATA 12.0 software. Eleven clinical case-control studies with a total of 636 NAFLD cases and 918 healthy controls met the inclusion criteria. Our meta-analysis results revealed that MTP -493G>T polymorphism was strongly correlated with an increased risk of NAFLD. Subgroup analysis by ethnicity suggested that MTP -493G>T polymorphism might increase individuals' susceptibility to NAFLD among both Caucasian and non-Caucasian populations. No publication bias was observed in this meta-analysis. In short, the present meta-analysis indicates that MTP -493G>T polymorphisms may contribute to individuals' susceptibility to NAFLD. Thus, MTP -493G>T polymorphism may be a valuable and practical biomarker for early detection of NAFLD.

CD226 rs763361 (Gly307Ser) polymorphism is associated with susceptibility to rheumatoid arthritis in Zahedan, southeast Iran

BACKGROUND

Rheumatoid arthritis (RA) is a chronic inflammatory disease with many genetic factors predisposing to disease susceptibility. The aim of the present study was to investigate the impact of CD226 rs727088 and rs763361 polymorphisms and susceptibility to RA in a sample of the Iranian population.

METHODS

This case-control study was carried out on 100 patients with RA and 104 healthy subjects. The polymorphisms were determined using tetra amplification refractory mutation system-polymerase chain reaction assay.

RESULTS

The rs763361 (Gly307Ser) polymorphism increased the risk of RA in codominant, dominant and recessive-tested inheritance models (odds ratio [OR] = 3.18, 95% confidence intervals [95% CI] = 1.44-7.02, P = 0.004, CC vs. TT, and OR = 1.98, 95% CI = 1.10-3.57, P = 0.023, CC vs. CT-TT, and OR = 2.61, 95% CI = 1.26-5.37, P = 0.010, CC + CT vs. TT, respectively). In addition, the rs763361 T allele increased the risk of RA (OR = 2.06, 95% CI = 1.38-3.08, P<0.001). However, no significant difference was observed among the groups regarding CD226 rs727088 polymorphism (χ2 = 3.20, P = 0.202).

CONCLUSIONS

Our finding showed that CD226 rs763361, but not rs727088, gene polymorphism increased the risk of RA in a sample of the Iranian population.

Association between CDH1 and MSX1 Gene Polymorphisms and the Risk of Nonsyndromic Cleft Lip and/or Cleft Palate in a Southeast Iranian Population

Objective

Orofacial clefts such as cleft palate (CP) and cleft lip (CL) and/or cleft palate (CL/P) are the most common congenital anomalies of the head and neck. The aims of the present study were to evaluate the possible association between CDH1 (rs11642413 and rs16260) and MSX1 (rs12532 and rs3775261) gene polymorphisms and nonsyndromic cleft lip and/or cleft palate (NS-CL/P) in a sample of the Iranian population.

Design and Setting

This case-control study was performed on 100 subjects with NS-CL/P and 100 healthy unrelated control subjects. Tetra amplification refractory mutation system-polymerase chain reaction and multiplex polymerase chain reaction were used to detect the single-nucleotide polymorphisms.

Results

There was a significant difference between NS-CL/P subjects and control subjects regarding CDH1 rs16260 C > A polymorphism, and the rs16260 AC as well as the rs16260 AA genotypes were associated with NS-CL/P susceptibility (odds ratio [OR] = 3.02, 95% confidence interval [CI] =1.51 −6.00, P=.001; and OR = 8.05, 95% CI = 1.72–37.75, P=.002, respectively). No significant difference was found between the groups regarding CDH1 rs11642413 polymorphism. Although MSX1 rs3775261 polymorphism was not a risk factor for the disease, the rs12532 AG and rs12532 GG genotypes were associated with NS-CL/P risk (OR = 2.82, 95% CI = 1.55–5.15, P=.001; and OR = 8.42, 95% CI = 2.26–31.29, P=.004, respectively).

Conclusion

Our data suggest that CDH1 and MSX1 gene polymorphisms are risk factors for susceptibility to NS-CL/P in a sample of the Iranian population. Larger studies are required to validate our findings.

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

Background

It 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 methods

This 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.

Results

There 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).

Conclusion

Our 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.

CD209 promoter -336 A/G (rs4804803) polymorphism is associated with susceptibility to pulmonary tuberculosis in Zahedan, southeast Iran

INTRODUCTION

The association between -336 A/G polymorphism of CD209 and susceptibility to/protection from tuberculosis is inconsistent.

AIM

The present study aimed at evaluating the possible association between CD209 rs4804803 (-336 A/G) gene polymorphism and pulmonary tuberculosis (PTB) in a sample of Iranian population.

MATERIALS AND METHODS

This case-control study was performed on 156 PTB patients and 154 healthy individuals. Tetra-amplification refractory mutation system-polymerase chain reaction was used to detect the polymorphisms.

RESULTS

Our findings revealed that the CD209 rs4804803 increased the risk of PTB in codominant [odds ratio (OR) = 5.16, 95% confidence interval (CI) = 1.60-16.59, p = 0.006, GG vs. AA], dominant (OR = 1.69, 95% CI = 1.07-2.66, p = 0.024, AG + GG vs. AA), and recessive (OR = 4.20, 95% CI = 1.34-13.16, p = 0.014, GG vs. AA + AG) tested inheritance models. Furthermore, the rs4804803 G allele increased the risk of PTB (OR = 1.58, 95% CI = 1.12-2.23, p = 0.011) as compared to the A allele.

CONCLUSION

Our data suggest that CD209 rs4804803 polymorphism increased the risk of PTB in a sample of Iranian population.

Association of Adiponectin rs1501299 and rs266729 Gene Polymorphisms With Nonalcoholic Fatty Liver Disease

BACKGROUND

Genetic and environmental factors are important for the development of nonalcoholic fatty liver disease (NAFLD). Adiponectin is a white and brown adipose tissue hormone, and have been found to play essential roles in the regulation of energy homoeostasis. Recent reports have identified a possible role of adiponectin in NAFLD via PPARγ pathway.

OBJECTIVES

The present study was designed to find out the impact of adiponectin rs1501299 (276G/T) and rs266729 (-11377C/G) gene polymorphisms in NAFLD.

PATIENTS AND METHODS

Eighty-three patients with diagnosis of NAFLD, and 93 healthy subjects were included in the study. Tetra ARMS-PCR was designed to detect single nucleotide polymorphisms.

RESULTS

A significant difference was found between NAFLD and control group regarding the rs266729 polymorphism (χ2 = 7.35, P = 0.025). The rs266729 polymorphism increased the risk of NAFLD in codominant (CC vs. CG: OR = 2.18, 95% CI = 1.16 - 4.12, P = 0.016) and dominant (CC vs. CG/GG: OR = 2.31, 95% CI = 1.25 - 4.27; P = 0.008) inheritance tested models. The G allele increased the risk of NAFLD (OR = 1.63, 95% CI = 1.03 - 2.57, P = 0.037) in comparison with C allele. No significant difference was found between the groups concerning adiponectin rs1501299 gene polymorphism (χ2 = 0.70, P = 0.697).

CONCLUSIONS

adiponectin rs266729 polymorphism might be a candidate gene, which determines the susceptibility to NAFLD. Larger studies are necessary to confirm these findings in various populations.

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 IRGM polymorphisms and susceptibility to pulmonary tuberculosis in Zahedan, Southeast Iran

Tuberculosis (TB) is a major cause of morbidity and mortality worldwide. IRGM1 is an important protein in the innate immune response against intracellular pathogens by regulating autophagy. Polymorphisms in the IRGM genes are known to influence expression levels and may be associated with outcome of infections. This case-control study was done on 150 patients with PTB and 150 healthy subjects to determine whether the IRGM polymorphisms at positions -1208 A/G (rs4958842), -1161 C/T (rs4958843), and -947 C/T (rs4958846) were associated with PTB. The polymorphisms were determined using tetra-amplification refractory mutation system-PCR (T-ARMS-PCR). The results showed that the IRGM -1161 C/T and -947 C/T polymorphisms were associated with decreased susceptibility to PTB (OR = 0.06, 95% CI = 0.03-0.13, P < 0.001 and OR = 0.27; 95% CI = 0.013-0.55, P < 0.001, resp.). No significant difference was found among the groups regarding -1208 A/G polymorphism. In conclusion we found that the IRGM -1161 C/T and -947 C/T polymorphisms but not -1208 A/G polymorphism provide relative protection against PTB in a sample of Iranian population.

Polymorphism in glutamate cysteine ligase catalytic subunit (GCLC) is associated with sulfamethoxazole-induced hypersensitivity in HIV/AIDS patients

Background

Sulfamethoxazole (SMX) is a commonly used antibiotic for prevention of infectious diseases associated with HIV/AIDS and immune-compromised states. SMX-induced hypersensitivity is an idiosyncratic cutaneous drug reaction with genetic components. Here, we tested association of candidate genes involved in SMX bioactivation and antioxidant defense with SMX-induced hypersensitivity.

Results

Seventy seven single nucleotide polymorphisms (SNPs) from 14 candidate genes were genotyped and assessed for association with SMX-induced hypersensitivity, in a cohort of 171 HIV/AIDS patients. SNP rs761142 T > G, in glutamate cysteine ligase catalytic subunit (GCLC), was significantly associated with SMX-induced hypersensitivity, with an adjusted p value of 0.045. This result was replicated in a second cohort of 249 patients (p = 0.025). In the combined cohort, heterozygous and homozygous carriers of the minor G allele were at increased risk of developing hypersensitivity (GT vs TT, odds ratio = 2.2, 95% CL 1.4-3.7, p = 0.0014; GG vs TT, odds ratio = 3.3, 95% CL 1.6 – 6.8, p = 0.0010). Each minor allele copy increased risk of developing hypersensitivity 1.9 fold (95% CL 1.4 – 2.6, p = 0.00012). Moreover, in 91 human livers and 84 B-lymphocytes samples, SNP rs761142 homozygous G allele carriers expressed significantly less GCLC mRNA than homozygous TT carriers (p < 0.05).

Conclusions

rs761142 in GCLC was found to be associated with reduced GCLC mRNA expression and with SMX-induced hypersensitivity in HIV/AIDS patients. Catalyzing a critical step in glutathione biosynthesis, GCLC may play a broad role in idiosyncratic drug reactions.

Bi-directional PCR allele-specific amplification (bi-PASA) for detection of caspase-8 -652 6N ins/del promoter polymorphism (rs3834129) in breast cancer

Caspase-8 (CASP8) plays a critical role in regulating apoptosis, and its functional polymorphisms may modify cancer risk. We investigated the possible association between CASP8 -652 6N ins/del (rs3834129) and the risk of breast cancer in a sample of Iranian population. This case-control study was done on 236 breast cancer patients and 203 cancer free healthy female. We designed a rapid and simple bi-directional PCR allele-specific amplification (bi-PASA) for detection of CASP8 -652 6N ins/del polymorphism. The results showed that the CASP8 -652 6N del/dl genotype was inversely associated with breast cancer risk (OR=0.33, 95% CI=0.17-0.65, p=0.001). The frequencies of the del allele in cases and controls were 29.1% and 38.6%, respectively. An inverse association between CASP8 6N del variant and the risk of breast cancer (OR=0.66, 95% CI=0.66-0.87, p=0.002) was found. In conclusion, the result suggests that the CASP8 -652 6N del polymorphism plays a protective role in susceptibility to breast cancer in our population. Further studies in other populations with larger samples are needed to confirm these findings.

R620W functional polymorphism of protein tyrosine phosphatase non-receptor type 22 is not associated with pulmonary tuberculosis in Zahedan, southeast Iran

The protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene, which encodes an intracellular lymphoid-specific phosphatase, is considered an important regulator of T-cell activation. We investigated a possible association between the PTPN22 C1858T (R620W) polymorphism and pulmonary tuberculosis in an Iranian population. Single nucleotide polymorphisms of PTPN22 C1858T (rs2476601) were genotyped in 172 pulmonary tuberculosis cases and 204 normal subjects from Zaheden, Iran. Frequencies of genotypes CC, CT and TT of the PTPN22 C1858T polymorphism were 98.3, 1.7 and 0% in the pulmonary tuberculosis patients, and 96.1, 3.9 and 0% in the control group, respectively (P = 0.239). The frequency of the minor (T) allele was 0.8% in pulmonary tuberculosis patients and 2.0% in controls. Significant differences were not observed in genotype or allele frequencies of PTPN22 C1858T in the comparison between pulmonary tuberculosis patients and healthy subjects in our Iranian population sample.

A tetra-primer amplification refractory mutation system-polymerase chain reaction for the detection of rs8099917 IL28B genotype

Two single nucleotide polymorphisms (SNP, rs8099917, rs12979860) near the IL28B gene have been illustrated as outcome predictors of hepatitis C virus (HCV) treatment with pegylated interferon/ribavirin. The aim of the present study was to design a simple tetra-primer amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) for the evaluation of the rs8099917 IL28B gene polymorphism. We efficiently designed a T-ARMS-PCR for detection of rs8099917 IL28B. Using this method, we genotyped 83 subjects with NAFLD (nonalcoholic fatty liver disease) and 93 healthy subjects. No significant differences were found in allelic and genotypic frequencies of rs8099917 IL28B gene polymorphism between NAFLD subjects and controls. The frequency of minor allele (G allele) was 0.13 in healthy and 0.19 in NAFLD subjects. In conclusion, we designed a simple, inexpensive, and reproducible T-ARMS-PCR for detection of rs8099917 IL28B polymorphism which can be used for routine assay. In addition, we found that rs8099917 polymorphism is not a risk factor for predisposition to NAFLD in a sample of Iranian population. Larger studies with different ethnics are required to validate our findings.

Genetic factors associated with the presence and progression of nonalcoholic fatty liver disease: a narrative review

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the world. Whereas insulin resistance and obesity are considered major risk factors for the development and progression of NAFLD, the genetic underpinnings are unclear. Before 2008, candidate gene studies based on prior knowledge of pathophysiology of fatty liver yielded conflicting results. In 2008, Romeo et al. published the first genome wide association study and reported the strongest genetic signal for the presence of fatty liver (PNPLA3, patatin-like phospholipase domain containing 3; rs738409). Since then, two additional genome wide scans were published and identified 9 additional genetic variants. Whereas these results shed light into the understanding of the genetics of NAFLD, most of associations have not been replicated in independent samples and, therefore, remain undetermined the significance of these findings. This review aims to summarize the understanding of genetic epidemiology of NAFLD and highlights the gaps in knowledge.

Association of genetic polymorphisms of glutathione-S-transferase genes (GSTT1, GSTM1, and GSTP1) and susceptibility to nonalcoholic fatty liver disease in Zahedan, Southeast Iran

Oxidative damage is thought to play a pivotal role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Glutathione-S-transferases (GSTs) are involved in cell protection against oxidative stress. We examined whether GSTM1, GSTT1, and GSTP1 polymorphisms are associated with NAFLD in a sample of the Iranian population. The current case-control study included 83 patients with NAFLD and 93 healthy subjects. The GSTM1 and GSTT1 polymorphisms were analyzed by multiplex polymerase chain reaction (PCR). The GSTP1 polymorphism was detected by tetra amplification refractory mutation system-PCR assay. The GSTM1-null genotype was significantly associated with the development of NAFLD (odds ratios [OR]=2.171, 95% confidence intervals [CI]=1.188-3.970, p=0.015). The GSTP1 Val allele was shown to be a risk factor for NAFLD (OR=1.739, 95% CI=1.089-2.777, p=0.024). The GSTT1 polymorphism was not significantly different between control and patient groups (p=0.221). This study showed that GSTM1 and GSTP1, but not GSTT1, genetic polymorphisms are associated with NAFLD in a sample of the Iranian population, and may be used to determine the risk of development of NAFLD.