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Neuronal ceroid lipofuscinoses type 2 (CLN2), the most common form of Batten disease, is caused by TPP1 loss of function, resulting in tripeptidyl peptidase-1 enzyme deficiency and cerebral accumulation of lipopigments. Clinical hallmarks include epileptic seizures, vision loss, progressive movement disorder, ataxia, and eventually death. Diagnosis is often delayed due to the rarity of the conditions. Results: Here, we report a case presenting with clinical features of CLN2, carrying a homozygous novel nonsense variant in

Background: The importance of microbiome in the progression and development of colorectal cancer (CRC) has been discussed in the last decade. Like colon bacteria, other intestinal microorganisms, including archaea, could also be involved in the CRC progression, so it's important to work out the archaeal microbiome (archaeome) composition among CRC patients. Objectives: The aim of this study was to determine the archaeome composition of CRC and healthy controls based on age and gender. Methods: Total bacterial DNA was extracted from 30 biopsy samples (17 CRC and 13 healthy controls). Archaeome communities were profiled by 16S rRNA high throughput sequencing, then compared to clinicopathological features, including CRC patients’ gender and age. Results: In the CRC patients, archaeal methanogens including Methanobrevibacter (86%) and Methanomassiliicoccus (8%) were overrepresented at the genus level. In contrast in the healthy controls, only two genera of haloarchaea including Natronococcus (58%) and Haloterrigena (42%) were presented. The results showed that the number of archaeal genera in men is higher than women in both the CRC and healthy controls. moreover, our results showed that the most genera of archaea are present in the CRC-32-50 group, six archaeal genera. The differential abundance taxa analysis results showed significant differences between healthy controls and CRC patients (P ≤ 0.05). Conclusions: The high abundance of methanogens in the colon archaeome of CRC patients compared to healthy controls suggests that methanogens may be involved in CRC development.

Background: Colorectal cancer (CRC) is the third most common malignant tumor worldwide. Emerging evidence suggests that dysbiosis of the colon microbiome may be involved in CRC development. Objectives: The present study aimed to compare the composition and diversity of the colon microbiome by high-throughput 16S ribosomal RNA (rRNA) sequencing between CRC patients and healthy controls. Microbiome composition and diversity were also examined based on gender. Methods: The colon microbiome richness and diversity of samples from 17 CRC patients and 13 healthy controls were analyzed by 16S rRNA sequencing. Alpha and beta diversity were calculated to determine the differences in colon microbiome diversity. Results: Alpha and beta diversity showed significant differences between the CRC and healthy control groups regarding the microbiome. Our results showed that CRC samples had the highest richness and diversity. The total number (P ≤ 0.01), phylogenetic diversity (P ≤ 0.01), Chao1 (P ≤ 0.01), Shannon (P ≤ 0.05), and Simpson (P ≤ 0.01) indices were significantly higher in the CRC group than in the healthy control group. In addition, the comparison between females and males showed that the microbiome diversity was higher in the CRC female (CRC-F) group than in other groups. Prevotella, Fusobacterium, Akkermansia, Leptotrichia, Streptococcus, and Parabacteroides were more commonly observed in the CRC group, while Bacteroides, Enterobacteriaceae (unknown genus), Ruminococcus, and Campylobacter were more commonly observed in the healthy control group. Conclusions: This study showed differences between the CRC and healthy control groups regarding the diversity and composition of the colon microbiome, suggesting a contribution of the microbiome in the development and progression of CRC.

Neuronal ceroid lipofuscinoses type 2 (CLN2), the most common form of Batten disease, is caused by TPP1 loss of function, resulting in tripeptidyl peptidase-1 enzyme deficiency and cerebral accumulation of lipopigments. Clinical hallmarks include epileptic seizures, vision loss, progressive movement disorder, ataxia, and eventually death. Diagnosis is often delayed due to the rarity of the conditions. Results: Here, we report a case presenting with clinical features of CLN2, carrying a homozygous novel nonsense variant in TPP1 (NM_000391:c.C832T, (p.Q278*), rs1352347549). Moreover, we performed a comprehensive literature review regarding previously identified disease-causing TPP1 mutations and genotype-phenotype correlations. Conclusion: Depending on the type of mutation, different phenotypes are observed in patients with CLN2, suggesting that the severity of phenotypes is related to the genotype of the patients.

Tumor relapse is the main cause of breast cancer related deaths and metastasis due to epithelial–mesenchymal transition (EMT) having a critical role in this process. MAML1 is the main co activator of NOTCH signaling pathway and its role in EMT remains unknown. In this study, this role was evaluated through overexpression and knockdown study of MAML1 in MCF7 and MDA-MB-231 cells. MAML1 overexpression up regulated the epithelial and down regulated the mesenchymal markers. In addition, MAML1 silencing decreased epithelial and increased mesenchymal markers. Notch inhibition using γ-secretase inhibitor resulted in increased E-cadherin expression. MAML1 ectopic expression, further increased E-cadherin expression with inhibition of NOTCH signaling. Wound healing assay showed that MAML1 overexpression decreases the rate of migration, while MAML1 silencing increases this rate significantly. In conclusion, our data indicated that MAML1 negatively regulates EMT markers expression in breast cancer cells.

Objective Intrauterine growth restriction (IUGR) is one of the most important causes of the fetus and newborn mortality in the population. The aim of this study was to investigate the relationship between hTERT gene expression level and IUGR pregnancy in an Iranian population. Study design The hTERT expression was analyzed in 66 placenta samples consisting of 33 controls and 33 IUGRs, and compared by Real-Time Polymerase Chain Reaction (PCR). The results were statistically analyzed using SPSS software. Results There was no significant difference between the placentas samples of IUGR and healthy individuals for hTERT gene expression (p = 0.621). Conclusions To the best of our knowledge, the current investigation is the first study on the association between hTERT gene expression and IUGR in Iran. According to our results, there was no significant correlation between hTERT and IUGR etiology in this study. Surely, using more samples could provide more definite results on this matter in the future.

Background: Vesicoureteral reflux (VUR) disease is the most common type of urinary tract anomalies in children. Genetic risk factors may be associated with the etiology of VUR. The role of the Glutathione S-transferases (GSTs) as multifunctional enzymes is cellular oxidative stress handling. This is the first study aimed at evaluating the relative risk of GSTP1, GSTM1, and GSTT1 polymorphisms in VUR susceptibility in children and provides new important insights into the genetics of affected children. Methods: The study was done in 2013 in Sistan and Baluchestan University, eastern Iran. Genotyping of three GSTP1, GSTM1, and GSTT1 genes were determined using the multiplex polymerase chain reaction assay in 216 reactions for 72 VUR children and 312 reactions for 104 healthy controls. Results: The presence of GSTT1 deletion was associated with high risk of VUR in children, whereas GSTP1 and GSTM1 genotypes did not show the same effect. Furthermore, the combination of GSTT1/GSTM1 and GSTT1/ GSTP1 genotypes showed a significant influence on lower risk of VUR in children. Conclusion: Deletion of GSTT1 functional gene is a genetic risk factor causing VUR in children. Interestingly, the combination of GSTM1 and GSTP1 null genotypes with GSTT1 has shown a protective role against risk of GSTT1 deletion.

Background: Infertility is one of the common health issues around the world. The prevalence of male factor infertility among infertile couples is approximately 30%- 35%, of which genetic factors account for 15%. The family-based whole-exome sequencing (WES) approach can accurately detect novel variants. However, selecting an appropriate sample for data generation using WES has proven to be challenging in familial male infertility studies. The aim of this study was to identify types of pathogenic male infertility in cases of familial asthenozoospermia. Case: Two families with multiple cases were recruited for the purpose of WES. The study population included two affected cases in pedigree I and three affected cases in pedigree II. Two different variant callers (SAMtools and GATK) with a single-sample calling strategy (SSCS) and a multiple-sample calling strategy (MSCS), were applied to identify variant sites. Conclusion: In this study, we represented the results for variant prioritization of WES data without sequencing fertile siblings in the same pedigree by applying two different pipelines (homozygosity and linkage-based strategy). Using the aforementioned strategies, we prioritized annotated variants and generated a logical shortlist of private variants for each pedigree. Key words: Male infertility, Whole-exome sequencing, GATK, SAMtools.

Aberrant promoter methylation of CpG islands of tumor-suppressor genes has been recognized as one of the important tumor markers for cancer detection. The aim of this study was to investigate the promoter methylation status of protocadherin 10 (PCDH10), a tumor suppressor gene, in Iranian colorectal cancer (CRC) patients. Cancerous and the adjacent normal tissues obtained from 38 CRC patients were used to assess the methylation status of PCDH10 with Methylation Specific PCR, in addition, to study the expression level of this gene by quantitative PCR. The relationship between hypermethylation and the demographic characteristics of these patients was analyzed. The promoter methylation level of PCDH10 was statistically different between tumoral and normal tissues in CRC patients. Twenty-seven out of 38 patients showed hypermethylation with a sensitivity of 73% and a specificity of 97%. PCDH10 expression decreased in 15 cases (46%) as 16 cases (50 %) showed overexpression and 1 case (4%) had no changes. Not a significant association was reported between PCDH10 hypermethylation and the clinicopathological characteristics (P>0.05). Our results indicated that PCDH10 methylation has a critical function in CRC, with a nearly elevated sensitivity and a high specificity in the Iranian population, qualify it as a potential candidate biomarker. © 2019 Tehran University of Medical Sciences. All rights reserved. Acta Med Iran 2019;57(8):472-477.

Gastric cancer is one of the most common upper gastrointestinal malignancies. Some Iranian provinces, such as in the northern and northwestern areas, are at a high risk, whereas the central and western provinces are at a medium and the southern regions at low risk. This study was carried out to estimate the impact of the expression patterns of ASIC1 and IL-6 genes and the IL-6rs-174 and ASIC1rs 75624685 polymorphisms in the pathogenesis of gastric cancer. Materials and methods: Tetra-ARMS PCR was employed to analyze the polymorphism status of the ASIC1 and IL-6 genes with 85 paraffin-embedded tissue blocks from cases and 117 normal blood samples as controls. We also investigated mRNA expression levels of these genes in 12 cases and controls using real-time PCR. Results: Our results showed a significant association between expression of ASIC1 and elevated risk of gastric cancer (p

Neural cells derived from embryonic stem cells (ESCs) have potential usefulness for the treatment of neurodegenerative disorders. Modulation of intrinsic growth factors expression such as neurotrophins and their respective receptors by these cells is necessary to obtain functional neural cells for transplantation. In present study, we compared neural differentiation potential of two different media, NB + 5%ES-FBS + N2B27 and Ko-DMEM + 5%ES-FBS for conversion of mESC derived neural progenitors (NPs) into mature neural cells with emphasis on effect of the these two media on neurotrophins and their respective receptors expression. Immunofluorescence staining, RT-qPCR and western blot analysis showed that the expression of neuronal specific markers, MAP2 and Tuj-1, in NB + 5%ES-FBS + N2B27 medium was significantly higher than the other medium. Western blot assay revealed that the expression of BDNF and NGF increased significantly in mature neural cells obtained from NB + 5%ES-FBS + N2B27 medium but decreased in neural cells from Ko-DMEM + 5%ES-FBS medium compared to mESCs. TrkB protein was not detectable in mESCs but its expression increased in neural cells obtained from both media although its expression in NB + 5%ES-FBS + N2B27 medium was significantly higher than the other medium. In contrast to TrkB, p75NTR protein was detectable in mESCs and is remained constant in neural cells cultured in NB + 5%ES-FBS + N2B27 medium but decreased significantly in the other medium. In conclusion, our results indicated that NB + 5%ES-FBS + N2B27 medium promoted neural differentiation process of mESCs and caused enhancement of neurotrophins protein expression in addition to their cognate receptors.

Background and Aim: Resistance to trastuzumab has been a critical barrier to targeted therapy of HER 2-positive (Human Epidermal Growth Factor Receptor 2) breast cancers. MicroRNAs (miRNAs) are known as decisive core regulators of drug resistance that modulate the epithelial-to-mesenchymal transition (EMT) and cancer-related immune responses. The present study aimed at examining the expression of miR-141 in trastuzumab-resistant and trastuzumab-sensitive BT-474 breast cancer cells. Materials and Methods: In this experimental study, trastuzumab-resistant BT-474 cells were generated by continuous in-vitro culture of BT-474 cells in the presence of trastuzumab for six months. The relative expression of miR-141 to U6 RNA was then evaluated in trastuzumab-resistant and trastuzumab-sensitive cells using Relative Real-Time PCR. Mann-Whitney test was used to compare the difference between the two groups. Results: There was a significant difference between the survival rates of resistant BT-474 cells and sensitive cells in the MTT test in the presence of different concentrations of trastuzumab showing that BT-474 breast cancer cells have turned resistant to this drug under long-term culture (P=0.001). Also, the expression of miR-141 in trastuzumab-resistant cells was significantly reduced by four times compared with the BT-474 parent cells (P=0.049). Conclusion: Down-regulation of miR-141 in trastuzumab-resistant BT-474 cells might be one possible mechanism for resistance against trastuzumab and an indication of the role of this microRNA in controlling the metastasis pathway. &nbsp

BACKGROUND: Intrauterine growth restriction (IUGR), a pathologic diminution of the rate of fetal growth, has been associated with alterations in expression of several genes. However, the role of long non-coding RNAs (lncRNAs) in its pathogenesis has not been studied. METHODS: In this study we evaluated the expression of four lncRNAs namely, nuclear paraspeckle assembly transcript (NEAT1), taurine up-regulated 1 (TUG1), p21-associated ncRNA DNA damage-activated (PANDA), and metastasis-associated lung adenocarcinoma transcript-1 (MALAT1) in placenta samples obtained from IUGR and normal pregnancies to determine their possible contributions in the pathogenesis of IUGR. RESULTS: We found no significant differences in expression levels between cases and controls. We also found no correlation between expression and clinical data of study participants; however, we found significant correlations between expression levels of all the assessed lncRNAs in both cases and controls. CONCLUSION: These results imply the existence of a possible shared regulatory mechanism for the expression of these transcripts in placenta. Future studies are needed to perform such evaluations in larger sample sizes or in animal models in earlier stages of pregnancy.

Purpose Asthenozoospermia (ASZ) is a condition characterized by reduced sperm motility in semen affecting approximately 19% of infertile men. Major risk factors, particularly gene mutations, still remain unknown. The main aim of the present study was to identify novel genes and mutations that may influence human sperm motility. Methods Whole-exome sequencing (WES) was performed on a large pedigree of infertile men (n = 5) followed by bioinformatics analyses. Candidate pathogenic variants were screened in a control cohort of 400 ancestry-matched Iranian fertile men, 30 unrelated men with idiopathic ASZ, and public databases. Results A rare mutation in GFPT2 gene (c.1097G > A; p.Arg366Gln) located in the SIS 1 domain was segregated with the phenotype and was consistent with autosomal recessive inheritance. The in silico analyses revealed that the mutation might affect the function of SIS 1 domain and abolish its carbohydrate-binding ability. Conclusion Homozygosity of the GFPT2 p.Arg366Gln mutation was associated with increased levels of reactive oxygen species (ROS) in spermatozoa and decreased sperm motility.

Resistance to trastuzumab has become a limiting factor for therapeutic efficacy of human epidermal growth factor 2 (HER2)-positive breast cancer. Different expression levels of miRNAs in cancer cells have been associated with poor prognosis and response to chemotherapy. The aim of this study was to evaluate miRNAs that were thought to be associated with HER2-positive breast cancer chemoresistance. In this study, the relative expression of candidate miRNAs to U6 RNA was evaluated in trastuzumab-resistant and trastuzumab-sensitive cells using relative real-time PCR. Our results demonstrated that miR-23b-3p, miR-195-5p, miR-656-5p, and miR-340-5p were significantly dysregulated. For the first time in this study, these miRNAs were identified to be involved in trastuzumab resistance. TargetScan and miRDB were then used for predicting the potential targets of the candidate miRNAs. Our results also revealed that the predicted potential targets of these miRNAs were strongly associated with drug resistance pathways. As a relative expression of candidate miRNAs was statistically different in trastuzumab-resistant and trastuzumab-sensitive cells, their potential targets were involved in drug resistance pathways. We strongly hypothesized the dysregulation of miRNAs as a possible mechanism of trastuzumab resistance. We also assumed that the strategic manipulation of these regulatory networks might be a possible therapeutic strategy to improve the results of chemotherapy for this resistance. However, more research is needed to evaluate the role of these miRNAs in the acquisition of trastuzumab resistance.

Hashimoto's thyroiditis (HT) is a chronic inflammation of the thyroid gland and is known as the most common autoimmune disease. Development of autoimmune destruction of thyroid cells is a multi-step process involving convergence of genetic and environmental factors. Cytotoxic T-lymphocyte antigen-4 (CTLA-4) has an important role in homeostasis and negative regulation of immune responses, and is therefore considered to be a key element in the development of autoimmune diseases. The present study evaluated the association of the CTLA-4 gene polymorphisms 318C/T (rs5742909) and +49A/G (rs231775) with HT in an Iranian population (including 82 patients with HT and 104 healthy controls who were referred for routine premarital blood screenings). Genotyping was performed using the tetra-primer amplification refractory mutation system polymerase chain reaction technique. No significant differences were observed in genotype and allele frequencies in the single nucleotide polymorphisms (SNPs) between cases and controls. In the cases as well as in the controls, the TT genotype in the −318C/T polymorphism was absent and the predominant genotype was CC, while the predominant genotype for the +49A/G SNP was AA. As only few studies in this field have assessed Iranian and even Middle Eastern populations, additional studies with a higher number of samples are recommended to further assess the impact of −318C/T (rs5742909) and +49A/G (rs231775) polymorphisms of CTLA-4 on HT.

The aberrant DNA methylation of the tumor suppressor genes involved in DNA Damage Response (DDR) signaling and cell cycle regulation may lead to the tumorigenesis. Our purpose here is to analyze the promoter methylation and mRNA expression levels of LATS1 and LATS2 (LATS1/2) genes in OSCC. Promoter methylation status of LATS1/2 genes was evaluated in 70 OSCC paraffin-embedded tissues and 70 normal oral samples, using Methylation Specific PCR (MSP). LATS1/2 mRNA expression profiles were also investigated in 14 OSCC patients and 14 normal samples, using real-time PCR. In both candidate genes, promoter methylation assessment revealed significant relationship between cases and controls (OR = 2.24, 95 % CI = 1.40–3.54, P = 0.001; LATS1 and OR = 15.5, 95%CI = 3.64–64.76, P

Background Pterygium is the human eye lesion whose prevalence in the general population is estimated about 2%. The disease, in extreme phase, can lead to visual disturbance and eventually causes complete loss of vision due to the lesion growth over the papillary axis. Pterygium invasive tissue is a tumor-like tissue that is initially identified and then is attacked by cytotoxic T cells. Cytotoxic T lymphocyte associated antigen 4 (CTLA4), as a modulator molecule of the adaptive immune system, plays a critical role in maintaining peripheral T cell tolerance by diminishing its responsiveness and increasing its activation threshold. The aim of this study is to investigate the association between some epigenetic changes of the CTLA4 gene, such as promoter methylation and gene expression, and pathogenesis of pterygia. Materials and methods Genomic DNA was extracted from 75 formalin-fixed, paraffin-embedded tissues of pterygia and 70 specimens of normal conjunctiva from eyes without pterygium as the control group, collected from Sistan and Baluchestan population. CTLA4 gene promoter methylation was carried out by methylation-specific PCR technique. The gene expression analysis was done on extracted total RNA from 20 healthy and 23 pterygium tissue samples using Real-Time PCR technique. Results Promoter methylation changes of CTLA4 gene were not statistically different in patients with pterygium in comparison with healthy controls (OR = 1.614; 95% CI = 0.57–4.75; P value = 0.37). However, gene expression level of CTLA4 was remarkably different in patients and healthy controls (Mean ± SD: 1.343 ± 0.133 and 2.027 ± 0.219, respectively; P value = 0.009). Conclusion This is a credible evidence of CTLA4 gene expression in human eye tissue. This first hand attempt of investigating the association of epigenetic changes of the CTLA4 gene and pathogenesis of pterygia, indicated a significant intensification of the gene expression of CTLA4 in patients with pterygia. We suggest that increasing CTLA4 gene expression can be a trigger which promotes pterygium enlargement. However, further studies on more populations with larger sample sizes need to be done to verify this hypothesis in the future.

Background: Breast cancer is the most common malignancy in women. Breast Cancer Type 1 Susceptibility gene (BRCA1) is a tumor suppressor gene, involved in DNA damage repair and in 81% of the breast-ovarian cancer families were due to BRCA1. In some clinically investigated genes, the intragenic marker polymorphism is important and the screening of such mutations is faster by using short tandem repeat (STR) polymorphism. Individual polymorphism of STR is a good evidence for following inheritance of repeat polymorphism. Objective: The aim of this study was to evaluate three intragenic BRCA1 marker polymorphisms in families, which have two or more patients with breast/ovarian cancer in comparison to healthy women. Materials and Methods: A total of 107 breast and/or ovarian cancer patients and 93 unrelated healthy women with no clinical phenotype of any malignancy or familial cancer history constitute the study groups. Haplotyping analysis, at 3 intragenic BRCA1 microsatellite markers (D17S855, D17S1322 and D17S1323), were performed for all subject and control groups using labeled primers. Results: After fragment analysis, significance differences were observed as follows: two alleles of D17S855; allele 146 (p=0.02) and 150 (p=0.006), and two alleles of D17S1322, allele 121 (p=0.015) and 142 (p=0.043). These differences were compared with control group. There was significance difference in 8 di/tri allelic haplotypes in present experimental subjects. Some haplotypes were observed to have approximately twice the relation risk for breast cancer. Conclusion: According to recent results, assessment of presence or absence of mentioned alleles in BRCA1 microsatellite can be used for prognosis in individuals, suspected of having or not having the breast cancer.

Purpose. Pterygium is a serious eye problem in countries with high exposure to UV. However, despite numerous studies, the molecular etiology of pterygium is unclear. Recent studies have indicated thatLATS1andLATS2genes are involved in DDR signaling pathways against continuous UV exposure. Our aim was to evaluate theLATS1andLATS2promoter methylation with the risk of pterygium formation.Methods. We evaluated the promoter methylation status ofLATS1andLATS2using methylation-specific PCR technique. Also, mRNA expression ofLATS1andLATS2was assessed in 14 cases of pterygium and 14 normal specimens by real-time PCR.Results. Promoter methylation ofLATS1andLATS2was detected significantly between pterygium tissues and normal tissues [LATS1; OR = 4.9; 95% CI: 1.54 to 15.48,P=0.003;LATS2; OR = 7.1; 95% CI: 1.53 to 33.19,P=0.004]. The gene expression analysis showed a statistically significant difference between pterygium tissues and healthy controls for bothLATS1andLATS2(P<0.05).Conclusions. The data of this study is the first report regarding the effect of promoter methylation of theLATS1andLATS2in the pterygium. To confirm these data, doing further studies in various genetic populations with large sample sizes using advanced molecular techniques is proposed.

In addition to other factors regarding the disease susceptibility, genetic factors are the main causes of Hashimoto's thyroiditis (HT) disease. CTLA4 and PTPN22 are the most prominent genes involved in the immune system regulation, thus effective in the pathogenesis of autoimmune diseases. In the current study, the association of two polymorphisms of CTLA4 and PTPN22 genes, 1661A/G (CTLA-4 gene) and C1858T (PTPN22 gene), with HT was investigated by PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) technique. The effects of -1661A/G and C1858T polymorphisms on the mRNA and protein structures of CTLA-4 and PTPN22 were investigated by an in silico analysis. There was no significant difference between the genotype and allele frequencies of PTPN-22 gene polymorphism (rs2476601) in case and control groups. There was a positive association between the frequency of heterozygous genotype of CTLA4-1661A/G polymorphism (rs4553808) and HT (P = .04), but no association was seen regarding allele frequencies. In-silico analysis predicted that the transition of allele A to allele G would lead to the loss of some of the binding sites. Also, the structural analysis of C1858T transition effect on protein revealed a significant influence on PTPN-22 function. Our results showed that heterozygous genotype of -1661A/G CTLA4 gene variation might be related with the risk of HT.

Background: Nephropathic Cystinosis, the most common cause of renal Fanconi syndrome, is a lysosomal transport disorder with an autosomal recessive inheritance pattern. A large number of mutations in CTNS have been identified as causative to date. A 57 kb deletion encompassing parts of CTNS is most commonly identified in Caucasians but this allele has not been identified in individuals of Eastern Mediterranean, Middle Eastern, Persian, or Arab origin to date. Methods and Results: Implementing whole exome sequencing (WES) in a consanguineous Iranian family, we identified this large deletion affecting CTNS in a patient initially presenting with hypokalemic metabolic alkalosis symptoms and considerable proteinuria. Conclusion: We show WES is a cost and time efficient genetic diagnostics modality to identify the underlying molecular pathology in Cystinosis individuals and provide a summary of all previously reported CTNS alleles in the Middle east population. Our work also highlights the importance to consider the 57-kb deletion as underlying genetic cause in non-European populations, including the Middle East. Limited diagnostic modalities for Cystinosis in developing countries could account for the lack of previously reported cases in these populations carrying this allele. Further, our findings emphasize the utility of WES to define genetic causes in clinically poorly defined phenotypes and demonstrate the requirement of Copy number variation (CNV) analysis of WES data.

Schizophrenia, with incidence of 1% worldwide, is a common mental disorder. Phosphoinositide-3-kinases (PI3Ks) are a family of enzymes involved in cellular functions such as cell growth, proliferation, differentiation, motility, intracellular trafficking, and survival. These enzymes play an important role in the PI3K/AKT signalling pathway. The PIK3CA gene encodes the alpha catalytic subunit of the PI3K enzyme. The present study analysed the role of three SNPs of the PIK3CA gene (rs6443624 (A/C), rs7640662(C/G) and rs7621329(C/T)) in the development of schizophrenia.In this case-controlled study, DNA was extracted from blood samples from 108 patients with schizophrenia and 108 healthy patients as controls. Genotypic analyses of PIK3CA SNPs rs6443624 (A/C), rs7640662(C/G) and rs7621329(C/T) were made using the tetra primer ARMS-PCR technique.The outcome shows significant difference between CT and the combined genotype (CT + TT) of rs7621329 and the risk of schizophrenia (OR = 6.4, 95% CI = 3.023-14.23, p 0.0001). Outcome showed no significant difference for were for analyses of the rs6443624 and rs7640662 genotypes.These results indicate an association between PIK3CA gene polymorphism on the rs7621329(C/T) site and the risk of schizophrenia. Further study of the genetic population using a larger sample size is necessary in order to validate these present findings.

Congenital factor XIII deficiency is a very rare bleeding disorder, but because of the high rate of consanguineous marriages, it is common in Sistan and Baluchestan Province of Iran. The discovery of promoter hypermethylation of numerous miRNAs in human diseases has demonstrated an epigenetic mechanism for aberrant miRNA expression. The present study has analyzed methylation and expression status of miR-185 and miR-132 genes in patients with inherited factor XIII deficiency in a sample of South-Eastern Iranian population. Promoter methylation of miR-185 and miR-132 was investigated by Methylation Specific Polymerase Chain Reaction (MS PCR) in blood samples of 75 factor XIII deficient individuals and 74 healthy controls. Expression level of these genes was also assessed in 15 blood samples of patients and 15 healthy controls using real-time quantitative reverse transcription PCR. Analysis of miR-132 and miR-185 promoter hypermethylation did not show any significant difference between cases and controls. Relative gene expression analysis in cases (n=15) with congenital factor XIII deficiency and healthy controls (n=15) revealed no statistically significant relationship for miR-132 (p = 0.126) and miR-185 (p = 0.165) genes. Our findings indicated that promoter methylation as well as gene expression of miR-132 and miR-185 had no significant effect on etiology of factor XIII deficiency.

Background and Aim There is evidence that gastric cancer patients suffer from thyroid disorders. However, the relationship between thyroid receptor (TR) expression and gastric cancer remains unknown. The aim of this study was to evaluate the status of promoter methylation and expression of the thyroid hormone receptor beta (THRβ) gene in gastric cancer patients in an Iranian population. Methods Analysis of THRβ promoter methylation was performed on 85 pairs of formalin-fixed, paraffin-embedded (FFPE) tissue samples as cases and controls via methylation-specific polymerase chain reaction (PCR [MSP]). The samples were obtained from tumors and surrounding healthy tissues from resected gastric cancers. The expression assay was also performed with 25 FFPE tissue pairs (tumor and surrounding healthy tissues of the same individual) using real-time PCR. Results The results of the present study show that there is a statistically significant difference between tumor and adjacent normal tissues regarding promoter methylation status and THRβ expression (P = 0.04 and P = 0.036, respectively). Conclusion Therefore, promoter methylation of THRβ may be involved in the development of gastric cancer.

Background: Drug addiction is a brain disorder that has negative consequences for individuals and society. Addictions are chronic relapsing diseases of the brain that are caused by direct drug-induced effects and persevering neuroadaptations at the epigenetic, neuropeptide and neurotransmitter levels. Because the dopaminergic system has a significant role in drug abuse, the purpose of this study was to analyze the methylation and expression profile of brain-derived neurotrophic factor (BDNF) and dopamine transporter (DAT1) genes in individuals with drug addiction. Materials and Methods:BDNF and DAT1 promoter methylation were investigated with a methylation-specific polymerase chain reaction (PCR) technique in blood samples from 75 individuals with drug addiction and 65 healthy controls. The expression levels of BDNF and DAT1 were assessed in 12 mRNA samples from the blood of patients and compared to the samples of healthy controls (n = 12) with real-time quantitative reverse transcription PCR. Results: No significant differences were found in the methylation of BDNF and DAT1 between patients and controls, but the relative levels of expression of BDNF and DAT1 mRNA differed significantly in the patients compared to controls (p < 0.0001). Conclusion: These results showed that the methylation status of the BDNF and DAT1 genes had no significant function in the processes of drug addiction.

Background: Apoptosis is an important mechanism that is responsible for the physiological deletion of harmful, damaged, or unwanted cells. Changed expression of apoptosis-related genes may lead to abnormal cell proliferation and finally to tumorigenesis. Our aims were to analyze the promoter methylation and gene expression profiles of FADD and FAS genes in risk of OSCC. Material and Methods: we analyze the promoter methylation status of FADD and FAS genes using Methylation - Specific PCR (MSP) in 86 OSCC tissues were kept in paraffin and 68 normal oral tissues applied as control. Also, FADD and FAS genes expression were analyzed in 19 cases and 20 normal specimens by Real-Time Reverse- Transcripts PCR. Results: Aberrant promoter methylation of FADD and FAS genes were detected in 12.79 % (11 of 86) and 60.46 % (52 of 86) of the OSCC cases, respectively, with a significant difference between cases and healthy controls for both FADD and FAS genes ( P

Background/Aim: It has been believed that epigenetic changes play a critical role in schizophrenia through improper interaction between genome and environmental risk factors. The aim of this case-control study was to investigate the association of the promoter hypermethylation status of glutathione S-transferase T1 (GSTT1) and glutathione S-transferase P1 (GSTP1) genes with the risk of schizophrenia. Materials and Methods: Methylation-specific PCR was used to estimate DNA methylation in the blood of 80 patients with schizophrenia and 71 healthy controls. Results: Promoter hypermethylation analysis of GSTT and GSTP indicated a significant difference between individuals with methylated and unmethylated status [odds ratio (OR) = 0.339, 95% confidence interval (95% CI) = 0.14-0.8, p = 0.012 and OR = 0.308, 95% CI = 0.135-0.7, p = 0.005, respectively]. Conclusion: The present study supports the hypothesis that impairment in the promoter region of GSTT and GSTP genes by hypermethylation may increase the risk of schizophrenia.

The aim this work is to estimate whether genetic polymorphisms of +874 of IFN-γ and -137 G/C,-607 C/A of IL-18 genes are implicated in the development of VUR, because a vast literature indicates that genetic variations play a significant role in the pathogenesis of VUR.The PCR single specific primer (SSP) and amplification refractory mutation system (ARMS) were applied for analyzing the polymorphic sites of -137 G/C,-607 C/A of IL-18 and +874 of IFN-γ genes in 110 healthy controls and 124 VUR children.A significant relationship was found between AT and combined AT + TT genotypes of IFN-γ and highly increased risk of VUR (OR = 4.2, 95% CI, 2.00-9.24; p 0.0001: OR = 4.00, 95% CI, 1.90-8.70, p 0.0001, respectively). On the other hand, the genotype frequency of IL18-137 G/C indicated a significant assessment of the decrease risk of VUR for GC and GC + CC genotypes (OR = 0.53, 95% CI, 0.3-0.9; p = 0.02: OR = 0.53, 95% CI, 0.3-0.92 p = 0.01, respectively). No significant association was found between -607 C/A polymorphism of IL-18 and UVR.To the author's best knowledge, this is the first data regarding polymorphism of IFN-γ (+874) cytokine genes that highly increased the risk of VUR. To confirm the presented data, further studies should be done in different populations with a larger sample size.

OBJECTIVE Schizophrenia (SCZ) is a type of psychotic disorder that affects ~1% of the population. Dopamine is one of the major neurotransmitters in the brain and its receptors are associated with a number of psychotic disorders, including SCZ. The aims of the present study were to analyze methylation and the expression profile of dopamine receptor DRD1, DRD2, DRD4, and DRD5 genes in patients with SCZ. MATERIALS AND METHODS Promoter methylation of DRD1, DRD2, DRD4, and DRD5 genes was assayed by a methylation-specific PCR in blood samples obtained from 80 SCZ cases and 71 healthy controls. Also, we investigated DRD1, DRD2, DRD4, and DRD5 mRNA levels using real-time reverse transcription PCR in 34 blood samples of healthy controls and cases. RESULTS Promoter methylation of DRD4, DRD5, and DRD2 genes was statistically different in cases compared with healthy controls. The mRNA expression level results also showed statistically significant differences (P

Objective: To investigate the effect of promoter methylation of cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) gene and matrix metalloproteinases (MMPs) on the risk of non-alcoholic fatty liver disease (NAFLD). Materials and Methods: CTLA-4 and MMP-9 promoter methylation were investigated using a methylation-specific polymerase chain reaction (MS-PCR) in blood samples taken from 80 NAFLD individuals and 95 healthy controls. The expression levels of CTLA-4 and MMP-9 were also assessed in 10 blood and 9 liver tissues mRNA samples from NAFLD patients. These cases were compared to the blood ( n = 10) samples of healthy controls with real-time quantitative reverse transcriptase PCR. Results: No significant relationship was found for methylation of CTLA-4 and MMP-9 between cases and controls. The relative expression of CTLA-4 and MMP-9 mRNA in NAFLD was not significantly different compared to healthy control samples. Conclusion: For the first time, our outcomes indicate that the methylation status of CTLA-4 and MMP-9 genes has no significant function on the process of NAFLD.

Background: Vesicoureteral reflux (VUR) is a common childhood disorder that is characterized by the abnormal movement of urine from the bladder into the ureters or kidneys. Objectives: The aim of this study was to determine whether the genetic polymorphisms of the IL-10, IL-12, and TNF-α genes are involved in the development of VUR. Patients and Methods: The tetra amplification mutation refractory system-polymerase chain reaction (Tetra-ARMS PCR) was applied to analyze the four polymorphic sites of the IL-10AG-1082, IL-10CA597, IL-12CA1188, and TNF308GA genes in 124 VUR children and 110 healthy controls. Results: A significant, highly increased risk of VUR disease was found for the CA, AA, and combined genotypes of IL-10CA597 (OR = 5.2, 95% CL: 1.80 - 18.25; P = 0.0006, OR = 9.1, 95% CL: 1.11 - 122.75; P = 0.02, OR = 5.3, 95% CL: 1.82 - 18.61; P = 0.00052, respectively); the AG, GG, and AG + GG genotypes of IL-10AG-1082 (OR = 12.8, 95% CL; 2.9 - 113.9; P = 0.00003, OR = 12.62, 95% CL: 2.93 - 114.53; P = 0.00003, respectively); and the AA genotype of IL-12 (AA, OR = 0.19, 95% CL: 0.5 - 0.55; P = 0.0006). The frequency of the C allele in both IL-10CA and IL-12CA was greater in patients with VUR than in the healthy controls. No association was found between TNF308GA and the risk of VUR. Conclusions: The results demonstrated significant associations between the IL-10 (AG-1089, IL-10CA) and IL-12 (AA) gene polymorphisms and a highly increased risk of VUR.

OBJECTIVES: Cervical cancer is rated the second most common malignant tumor globally and is etiologically linked to human papillomavirus infection. Interleukin-4 (IL-4) and IL-10 are cytokines with anti-inflammatory properties. The purpose of this study was to determine the relationship of different alleles of IL-4 and IL-10 genes with risk of cervical cancer among passive smokers and users of oral contraceptives. MATERIALS AND METHODS: We investigated the association of cervical cancer with 2 anti-inflammatory cytokine genes IL-4 and IL-10 using a case-control study. The study sample comprised 200 cases of cervical cancer and an equal number of matched controls who were investisgated by variable number of tandem repeat and Restriction Fragment Length Polymorphism analysis. RESULTS: In this study we observed that the Rp1/Rp2 genotype of IL-4 marginally increased the risk of developing cervical cancer [odds ratio (OR) 1.3; 95% confidence intervals (CI) 0.45-3.64; P=0.8]. In case of passive smokers we also found a marginal increase in the risk for cervical cancer with AC and combined AC+CC genotypes (OR 1.7; 95% CI 0.90-3.34; P=0.1; and OR1.7; 95% CI 0.90-3.17; P=0.1 respectively). However a nonsignificant association was observed between use of oral contraceptives and risk of cervical cancer with anti-inflammatory cytokine genotypes. CONCLUSIONS: This study suggests that passive smokers among North Indian women having IL-4 Rp1/Rp2 and IL-10 (AC) genotypes had an increased risk for developing cervical cancer.

Glutathione S-transferases (GSTs) are major intracellular antioxidants, which, impaired in their function, are involved in the progress of schizophrenia (SCZ). The aim of this case-control study was to investigate the association between the polymorphism of glutathione S-transferases M1 (GSTM1), T1 (GSTT1), the glutathione S-transferase P1 gene (GSTP1) and SCZ. We isolated genomic DNA from peripheral blood of 93 individuals with SCZ and 99 healthy control subjects' genotypes analyzing them for GSTM1, GSTT1 and GSTP1 using polymerase chain reaction. The analysis of the gene–gene interaction between GSTs indicated that the magnitude of the association was greater for the combined AG/GSTT1 & GSTM1 genotypes (OR = 2.51; 95% CI: 1.13–5.63, P = 0.02). The AG and combined AG + GG genotypes of GSTP1 increased the risk of SCZ (OR = 1.83; 95% CI: 0.94–3.75 and OR = 1.71; 95% CI: 0.92–3.19, respectively). The genotypes of GSTT/NULL, NULL/GSTM and NULL/NULL increased the risk of SCZ (OR = 2.05; 95% CI: 0.9–4.74; OR = 2.0; 95% CI: 1.68–2.31; and OR = 1.8; 95% CI: 0.57–2.46, respectively). The present study supports previous data that suggest that impairment in the function of GSTs genes may increase the risk of SCZ.

Summary Reactive oxygen species can affect many cellular functions through protein oxidation or initiation of the lipid peroxidation cascade that can lead to non-alcoholic fatty liver disease (NAFLD), characterized by significant lipid deposition in the hepatocytes of patients with no history of excess alcohol intakes. The present study aimed to analyze the methylation status of the antioxidative stress genes GSTT1 (glutathione S-transferase theta-1) and GSTP1 (glutathione S-transferase pi-1), and their expression profiles, in a sample population of patients with NAFLD living in South-East Iran. Patients and methods Peripheral blood samples were obtained from 80 NAFLD patients and 80 healthy controls. Promoter methylation of the GSTT1 and GSTP1 genes were analyzed by methylation-specific polymerase chain reaction (MS-PCR). Expression profiles of these genes were also examined by quantitative real-time PCR analysis. Results Promoter methylation of the GSTT1 gene was detected in 86.2% of cases and in 91.2% of controls and, of the GSTP1 gene, in 88.8 and 87.5% of cases and controls, respectively. Promoter methylation of GSTT1 and GSTP1 was not statistically different in cases compared with healthy controls. Similarly, mRNA expression levels showed no statistically significant variations between healthy individuals and patients with NAFLD. Conclusion Our findings indicate no association between methylation status and expression profiles of GSTT1 and GSTP1 genes and NAFLD. This is the first report to assess such associations in a sample of the Iranian population.