Whole-exome sequencing analysis in a case of primary congenital glaucoma due to the partial uniparental isodisomy.

We described a clinical, laboratory, and genetic presentation of a pathogenic variant of the CYP1B1 gene through a report of a case of primary congenital glaucoma and a trio analysis of this candidate variant in the family with the sanger sequencing method and eventually completed our study with the secondary/incidental findings. This study reports a rare case of primary congenital glaucoma, an 8-year-old female child with a negative family history of glaucoma and uncontrolled intraocular pressure. This case's whole-exome sequencing data analysis presents a homozygous pathogenic single nucleotide variant in the CYP1B1 gene (NM 000104:exon3:c.G1103A:p.R368H). At the same time, this pathogenic variant was obtained as a heterozygous state in her unaffected father but not her mother. The diagnosis was made based on molecular findings of whole-exome sequencing data analysis. Therefore, the clinical reports and bioinformatics findings supported the relation between the candidate pathogenic variant and the disease. However, it should not be forgotten that primary congenital glaucoma is not peculiar to the CYP1B1 gene. Since the chance of developing autosomal recessive disorders with low allele frequency and unrelated parents is extraordinary in offspring. However, further data analysis of whole-exome sequencing and sanger sequencing method were applied to obtain the type of mutation and how it was carried to the offspring.

Associations of the ANKK1 and DRD2 gene polymorphisms with overweight, obesity and hedonic hunger among women from the Northwest of Iran.

BACKGROUND: Pleasure from palatable foods can stimulate hedonic eating and, therefore, might be a major culprit for obesity. Dopamine receptor polymorphisms, especially variants in the genes regulating the D2 receptor, including ANKK1 and DRD2, are the prime candidates for assessing the individual differences in hedonic eating. This study was carried out to investigate the possible associations of the T (rs1800497) and Del (rs1799732) alleles with body mass index (BMI) and hedonic hunger among Iranian Azeri women. METHODS: A total of 372 healthy overweight/obese subjects (BMI ≥ 25 kg/m2) and 159 normal weight individuals (BMI 18.5-24.9 kg/m2) were genotyped for the polymorphisms of ANNK1 and DRD2 genes using PCR-RFLP. BMI and hedonic hunger were also evaluated. RESULTS: Three hundred and sixty-three (68.36%), 152 (28.63%), and 16 (3.01%) of the participants had CC, CT, and TT genotypes for ANNK1 gene, respectively. Of 515 samples genotyped for DRD2 gene, 315 (60.51%), 173 (33.59%), and 27 (5.24%) had Ins/Ins, Ins/Del, and Del/Del genotypes, respectively. The genotype and genotype frequencies were significantly different between the groups (p = 0.04). Significant differences were observed between the T+ genotype (TT + TC) and the T- genotype (CC) regarding the BMI and hedonic hunger scores (p < 0.05). In addition, Del+ group (Del/Del + Ins/Del) had higher BMI and hedonic hunger scores compared to Del- group (Ins/Ins) (p < 0.05). CONCLUSIONS: Our findings showed that the frequencies of T and Del alleles were greater in the overweight/obese individuals. Also, the polymorphism of ANKK1 (rs1800497) and polymorphism of the DRD2 gene (rs1799732) showed significant associations with BMI and hedonic hunger. LEVEL OF EVIDENCE: Level III, case-control study.

The effect of complement factor B gene variation on age-related macular degeneration in Iranian patients.

PURPOSE: To determine the possible association of rs4151667 (L9H) complement factor B (CFB) gene with age-related macular degeneration (AMD). The L9H is one of the functional variations of the CFB. CFB gene encodes the most important protein of the complement system. METHODS: Two hundred sixty-six patients with AMD and 194 unrelated age/sex-matched controls were genotyped for CFB gene (rs4151667) using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. All research subjects were selected from three regions of Iran (Tehran, Tabriz, and Gonabad). RESULTS: The results showed a significant difference between the frequency of non-TT genotype in total patients and controls [odds ratio (OR) = 0.424, P = 0.038]. The analysis for each studied region showed that in patients originating from the Gonabad population, the frequency of TT and non-TT genotypes between patients and the control group were significantly different (OR = 2.894, P = 0.046 for TT genotype and OR = 0.346, P = 0.026 for non-TT genotype). In patients originating from Tabriz population, TT and non-TT genotypes and A allele revealed considerably different frequencies between the patient and control groups (OR = 3.043, P = 0.017; OR = 0.329, P = 0.013 and OR = 0.347, P = 0.048, respectively). Analysis of patients from Tehran also showed that there was a significant difference in the frequency of TT genotype between patients and controls (OR = 2.168, P = 0.04). CONCLUSIONS: The results of the current study indicated a possible protective role for non-TT genotype in L9H variation CFB gene against AMD in a sample of the Iranian population. The region segregation results showed that TT genotype might be a risk factor for susceptibility to AMD.

Common chemotherapeutic agents modulate fatty acid distribution in human hepatocellular carcinoma and colorectal cancer cells.

Introduction: Cancer cells are critically correlated with lipid molecules, particularly fatty acids, as structural blocks for membrane building, energy sources, and related signaling molecules. Therefore, cancer progression is in direct correlation with fatty acid metabolism. The aim of this study was to investigate the potential effects of common chemotherapeutic agents on the lipid metabolism of hepatocellular carcinoma (HCC) and colorectal cancer (CRC) cells, with a focus on alterations in cellular fatty acid contents. Methods: Human HepG2 and SW480 cell lines as HCC and CRC cells were respectively cultured in RPMI-1640 medium supplemented with non-toxic doses of 5-fluorouracil and doxorubicin for 72 hours. Oil Red O dye was used to estimate intracellular lipid vacuole intensity. Fatty acid analysis of isolated membrane phospholipids and cytoplasmic triglycerides (TG) was performed by gas-liquid chromatography (GLC) technique. Results: Oil red O staining represented significantly higher lipid accumulation and density in cancer cells after exposure to the chemotherapeutic agents as compared to non-treated control cells. Doxorubicin and 5-fluorouracil treatment promoted the channeling of saturated fatty acids (SFAs) from phospholipids to triglyceride pool in both HepG2 (+5.91% and +8.50%, P < 0.05, respectively) and SW480 (+37.41% and +5.73%, P < 0.05, respectively) cell lines. However, total polyunsaturated fatty acid content was inversely shifted from TG to phospholipid fraction after doxorubicin and 5-fluorouracil incubation of HepG2 (+58.89% and +29.13%, P < 0.05, respectively) and SW480 (+19.20% and +14.65%, P < 0.05, respectively) cells. Conclusion: Our data showed that common chemotherapeutic agents of HCC and CRC can induce significant changes in cellular lipid accumulation and distribution of fatty acids through producing highly saturated and unsaturated lipid droplets and membrane lipids, respectively. These metabolic side effects may be associated with gastrointestinal cancers treatment failure.

Relationship of Serum Klotho Level With ACE Gene Polymorphism in Stable Kidney Allograft Recipients.

INTRODUCTION: The kidney is the main source of serum Klotho production. Immunosuppressive agents could affect the kidney in this regard. The effect of the ACE gene polymorphism on Klotho production is a less studied area. This study aimed to assess serum Klotho and ACE gene in a group of stable kidney transplant recipients. MATERIALS AND METHODS: In a cross-sectional study, 30 kidney transplant recipients with stable allograft function and 27 healthy young individuals were assessed for their serum Klotho levels. The ACE gene polymorphisms were studied in both groups. RESULTS: Klotho level was higher in kidney transplant recipients than the controls, but the difference was not significant (2.76 ± 2.41 ng/mL versus 2.01 ± 1.41 ng/mL, respectively). In both groups, serum Klotho level was higher in those with the I>I polymorphism, the men, those with higher glomerular filtration rate, and younger individuals, but the differences did not reach a significant level. Higher body mass index was significantly associated with lower serum Klotho level in both groups. CONCLUSIONS: Klotho level after kidney transplantation meets the range in healthy individuals, and it is not affected by the ACE gene polymorphism.

Association between proto-oncogene mutations and clinicopathologic characteristics and overall survival in colorectal cancer in East Azerbaijan, Iran.

BACKGROUND: Colorectal cancer (CRC) is the third-most common cancer in Iran. The increasing incidence of CRC in the past three decades has made it a major public health burden in the country. This study aimed to determine any relationship of specific mutations in CRCs with clinicopathologic aspects and outcome of patients. MATERIALS AND METHODS: This study was conducted on 100 CRC patients by the case-only method. Polymerase chain-reaction products were analyzed by Sanger sequencing, and sequence results were compared with the significant KRAS and BRAF gene mutations in the My Cancer Genome database. Logistic regression models were used to detect associations of clinicopathologic characteristics with each of the mutations. Kaplan-Meier and Cox regression models were constructed to estimate overall survival in patients. RESULTS: A total of 26 subjects (26%) had heterozygote-mutant KRAS, and mutations were not detected in the amplified exon of BRAF in both tumor and normal tissues of the 100 CRCs. Rectal tumors had 1.53-fold higher likelihood of KRAS mutations than colon tumors, and men had 1.37-fold higher odds than women. The presence of metastasis increased the likelihood of KRAS mutations 2.36-fold over those with nonmetastatic CRCs. Compared to patients with KRAS wild-type cancers, those with KRAS mutations had significantly higher mortality (hazard ratio 3.74, 95% confidence interval 1.44-9.68; log-rank P=0.003). CONCLUSION: Better understanding of the causality of CRC can be established by combining epidemiology and research on molecular mechanisms of the disease.

Gender Differences in Clinical Presentations of Cystic Fibrosis Patients in Azeri Turkish Population.

BACKGROUND: Cystic fibrosis (CF) is an autosomal recessive disorder with several clinical presentations. This study was undertaken in the Azeri Turkish population in Iran, to investigate gender differences in the age at onset and diagnosis, age of death, and duration of illness of CF. METHODS: The data of 331 CF patients from 2001 to 2015 was surveyed. Parameters including age, sex, ΔF508 mutation, age at onset, age at diagnosis, age of death and clinical presentations were evaluated for both sexes, using descriptive analysis. The association of gender with these variables was studied using logistic regression, chi-square test and Mann-Whitney U test by SPSS version 18. Odds ratio with a confidence interval of 95% and p≤0.05 was considered statistically significant. RESULTS: The study included 191 males (57.7%) and 140 females (42.3%), all showing statistically significant difference (p<0.001). Age duration differed between genders. Male and female patients were further under 9 and 4 years, respectively. The occurrence of ΔF508 mutation was 0.51 times more in females than in males. Age, diagnosis and sex were closely associated: males were diagnosed at a significantly later age than females (p=0.05). While this compression performed based on clinical presentations, males with respiratory disease had a later median age at diagnosis than females at lifespan (p=0.001). The risk of infertility in males was approximately two times greater than in females (p=0.02). CONCLUSION: These findings indicate gender differences in CF patients. Future studies are needed to establish other differences and evaluate the causes for the gender variations.

Association Between Outcomes and Demographic Factors in an Azeri Turkish Population With Cystic Fibrosis: A Cross-Sectional Study in Iran From 2001 Through 2014.

BACKGROUND: Outcomesforcystic fibrosis patients are improving rapidly. The demographic factors are notable variables inoutcomes, which can be evaluated and modified. OBJECTIVES: This study was designed to investigate the association between outcome and demographic factors in patients with cystic fibrosis. PATIENTS AND METHODS: This was a cross-sectional study and data were gathered for 331 patients using the census method, from March 2001 to September 2014 in Iran. Data was analyzed using logistic regression analysis, chi-square test, and independent sample t test using SPSS 18. Odds ratio with confidence intervals of 95% and P < 0.05 were considered significant. RESULTS: There were 85 (25.7%) deceased patients and 246 (74.3%) living patients at the time of the study. Of the 246 living CF patients, 202 (82.2%) were less than nine years of age, and 77 (90.6%) out of the 85 deceased CF patients had died younger than four years of age. There was a significant difference between outcome and location of residence. The risk of mortality was 50% less in urban patients than in rural patients (P = 0.03). The risk of mortality was approximately two times higher in patients with a positive family history than in those with a negative family history (P = 0.02). The proportion of mortality was approximately two times, or 94%, higher for those in a consanguineous marriage than for those in a non-consanguineous marriage (P = 0.01). CONCLUSIONS: The results demonstrated that the mortality rate was higher in CF patients with a positive family history, a consanguineous marriage, and residence in a rural area. Therefore, demographic factors play an important role in the outcome of cystic fibrosis. Unfortunately, these parameters, which can be managed easily and with low cost, have been overlooked.

Helicobacter pylori vacA i region polymorphism but not babA2 status associated to gastric cancer risk in northwestern Iran.

Helicobacter pylori-specific genotypes have been strongly associated with an increased risk of gastric cancer (GC). The aim of the present work was to study the associations of H. pylori virulence factors, vacA i region polymorphisms and babA2 status with GC risk in Azerbaijan patients. The DNA extracted from gastric biopsy specimens was used to access the babA2 and vacA genotypes. Overall, babA2 was present in 85.39 % (76/89) of H. pylori strains: 19 out of 24 (79.16 %) strains from GC, 16 out of 17 (94.14 %) strains from peptic ulcer disease (PUD) and 41 out of 48 (85.14 %) strains from chronic gastritis. No significant association was found between babA2 genotype and clinical outcomes (P > 0.05). i1 vacA polymorphism was detected in 46/89 (51.68 %) strains: in 21/24 (87.5 %), 6/17 (35.29 %) and 19/48 (39.58 %) patients with GC, PUD and chronic gastritis, respectively. i2 allele was detected in 43 (48.31 %) out of all 89 strains examined: 3 (14.28 %) of 24 strains from GC, 11 (64.71 %) of 17 from PUD, and 29 (60.42 %) of 48 strains from chronic gastritis. In this study, multiple linear regression analysis confirmed the strong association of i1 allele with GC (partial regression correlation 0.455 ± 0.101; P = 0). Results of multiple logistic regression analysis showed that vacA i1 genotype was significantly associated with GC compared with a control group (gastritis) (odds ratio 13.142, 95 % CI 3.116-55.430; P = 0). Findings from the measurement of H. pylori babA2 and vacA genotypes indicate a strong correlation between the vacA i1 allele and GC risk in the Azerbaijan area of Iran.

Tumor Necrosis Factor Gene Polymorphisms in Advanced Non-exudative Age-related Macular Degeneration.

PURPOSE: To investigate tumor necrosis factor (TNF)-α gene polymorphisms in advanced dry-type age-related macular degeneration (AMD) in a population from Northeastern Iran. METHODS: In this case-control study, 50 patients with geographic macular atrophy and 73 gender-matched controls were enrolled. Genomic deoxyribonucleic acid (DNA) was extracted from the peripheral blood. Polymerase chain reaction was performed to analyze 2 candidate single nucleotide polymorphisms in the TNF-α gene, namely -1031 thymine (T)/cytosine (C) and -308 guanine (G)/adenine (A). RESULTS: The distribution of the - 1031 T/C genotype was TT, 62%; TC, 36%; CC, 2% in the patients and TT, 60%; TC, 36%; CC, 4% in the controls (P = 0.94). Genotype analysis of TNF-α -308 also revealed no significant difference in distribution between patients (G, 78%; GA, 22%; AA, 0%) and controls (GG, 74%; GA, 23%; AA, 3%) (P = 0.51). None of the haplotypes nor alleles of studied TNF-α polymorphisms were significantly associated with advanced dry-type AMD. CONCLUSION: The findings of this study show that polymorphisms in the TNF-α gene, do not play an important role in dry-type AMD in the studied population.

FMF Genotype-phenotype correlation in Iranian Azeri Turks: Association between M694V/R761H mutation and amyloidosis.

OBJECTIVES: Familial Mediterranean fever (FMF), an inherited autosomal recessive disorder, is frequently present among individuals of Mediterranean origin. Differences in the clinical manifestations of FMF between different ethnic groups have been documented. The aim of the present study was to determine the most common characteristics of FMF and the relationship between clinical findings and the most common mutant alleles of the MEFV gene in an Iranian Azeri Turk population. MATERIALS AND METHODS: We analyzed clinical and genetic data from 415 patients identified as having FMF clinical symptoms and who were referred to the Molecular Genetics Laboratory of Tabriz/Iran over the last 3 years. The mutation type and clinical characteristics were determined for each patient. RESULTS: The following primary clinical characteristics of the patients were observed peritonitis was observed in 378 (93.8%), high-grade fever in 351 (86.88%), arthritis in 215 (54.57%), pleuritis in 207 (53.49%), myalgia in 153 (41.69%), AA amyloidosis in 149 (40.16%), and erysipelas-like erythema in 54 (14.96%) subjects. A positive response to colchicines treatment was noted in 374 (95.1%) patients including 303 patients with two mutated alleles and 71 patients with one identified mutation. CONCLUSION: In contrast to previous studies, there was no significant association between M694V mutation and development of amyloidosis. The M680I/M680I, M680I, M694I, and M694V/R761H genotypes were found to be associated with the development of amyloidosis. These results indicate that physicians need to pay careful attention to patients with asymptomatic or mildly symptomatic FMF with these genotypes.

MEFV mutations in Northwest of Iran: a cross sectional study.

OBJECTIVES: Familial Mediterranean Fever (FMF) is an autosomal recessive disorder characterized by recurrent episodes of fever accompanied by peritonitis, pleurisy, and arthritis. FMF affects mainly Mediterranean populations and is caused by mutations in the familial Mediterranean fever (MEFV) gene. The aim of this study was to identify the frequency and distribution of MEFV mutations in Iranian Azerbaijanis with FMF. MATERIALS AND METHODS: Medical records of 1330 Iranian Azerbaijanis who were diagnosed with FMF according to Tel-Hashomer criteria from May 2006 to April 2013 were reviewed and 10 MEFV mutations were found in affected individuals. RESULTS: 243 patients (18.27%) were homozygous, 370 (27.82%) were compound heterozygous and 717 (53.91%) were identified as heterozygous for one of the studied mutations. Of the studied mutations, M694V, E148Q, V726A, M680I, and M694I accounted for 42%, 21%, 19%, 14% and 2% of mutations respectively. CONCLUSION: In our study, M694V was found to be the most prevalent mutation. M694I, the most common mutation among Arabs, is rare in this cohort. Allele frequencies of the common mutations in our studied population have some similarities to those of the Turkish population reported previously. However, M680I is less common in our cohort.

Tumour necrosis factor-alpha gene polymorphisms in Iranian patients with biliary atresia.

BACKGROUND: Biliary atresia (BA) is a progressive inflammatory destructive process of the bile ducts. This study evaluated the relationship between single-nucleotide polymorphisms in the promoter region of tumour necrosis factor-alpha (TNF-α) gene and bilaiary atresia. MATERIALS AND METHODS: Genomic deoxyribonucleic acid from 16 patients with established diagnosis of BA and 36 patients with INC was obtained. The genotypes of TNF-α-1031 (T/C) and TNF-α-308 (G/A) were determined using the restriction fragment length polymorphism-polymerase chain reaction and the results were analysis with proper statistic software. RESULTS: The frequencies of T/T, T/C in TNF-α-1031 and G/G, G/A in TNF-α-308 were as same as control group. Moreover, we have same deduction for allele frequency and haplotypes analysis (T allele: 84.37%; G allele: 87.5%) in BA patients (T allele: 80.56%; G allele: 86.11%) in controls. In all cases variants of polymorphism did not affect the severity or incidence of BA disease. CONCLUSION: although no significant associations were found between BA and control groups, it seems meaningful that since the nature of BA is multi factorial. Next step will be considering a new target such as downstream modulation of the TNF-α pathway or other cytokines and chemokines which act directly/indirectly.

Helicobacter pylori vacA d1 genotype predicts risk of gastric adenocarcinoma and peptic ulcers in northwestern Iran.

BACKGROUND: There is a close relationship between Helicobacter pylori (H pylori)-specific factors and different gastroduodenal diseases. The present study aimed to investigate the prevalence of vacA d1, d2 genotypes in the H pylori isolates from patients with gastric adenocarcinoma, peptic ulcer disease (PUD) and gastritis in East Azerbaijan region, where the incidence of gastric cancer (GC) is high. Strains isolated from this area are likely to be of European ancestry. MATERIALS AND METHODS: In this study, genotyping of the vacA d region of 115 isolates obtained from patients with different gastrodoudenal diseases was accomplished by PCR methods. In addition to PCR amplification of H pylori 16S rDNA, rapid urease tests or histological examination were used to confirm the presence of H pylori in biopsy specimens. Data were collected and analyzed using SPSS version 19. RESULTS: Of the total of 83 H pylori isolates, 36 (43.4%) contained the d1 allele and 47 (56.6%) were subtype d2. The results of the multiple linear/logistic regression analysis showed high correlation between allele d1 and gastric adenocarcinoma or PUD. CONCLUSIONS: This study suggests that the H pylori vacA d1 genotype helps predict risk for gastric adenocarcinoma and PUD in East Azerbaijan, Iran.

Detection of human papillomavirus in the saliva of women with concurrent human papillomavirus related genital lesions.

OBJECTIVE: To determine the association of the human papillomavirus (HPV) subtypes in the saliva of women and HPV-related genital lesions. METHODS: In a cross-sectional study, 104 women with documented genital HPV-related lesions and known HPV status were selected. These cases were examined for the HPV subtypes in their salivary specimens from July 2006 to August 2009 at the Gynecologic Clinics of Alzahra Teaching Hospital, Tabriz, Iran. To detect HPV DNA subtypes of 16, 18, 31, 33, 6, and 11,HPV was genotyped by polymerase chain reaction assay. RESULTS: Type 16 HPV was the most frequently detected subtype in the saliva (29.8%), and cervix (24%). In addition, there was a significant association between the saliva and cervix with co-infection (p=0.009), and between the viral types of salivary and cervical+vulvar samples (p=0.00), and salivary and vulvar samples (p=0.001). On the other hand, there was a significant difference between the cervical and vulvar samples for the viral subtypes (p=0.000). CONCLUSION: The high risk HPV 16 is the most common simultaneous HPV subtype in the saliva and cervix of the cases. Identifying the HPV subtypes in saliva may facilitate recognizing persistent genital infections.

Molecular analysis of the SMN and NAIP genes in Iranian spinal muscular atrophy patients.

BACKGROUND: Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder characterized by degeneration of spinal cord anterior horn cells, leading to muscular atrophy. SMA is clinically classified into three subgroups based on the age of onset and severity. The majority of patients with SMA have homozygous deletions of exons 7 and 8 of the survival motor neuron (SMN) gene. The purpose of the present study was to determine the frequency of SMN and neuronal apoptosis inhibitory protein (NAIP) gene deletions in Iranian SMA patients. Experience in prenatal diagnosis of SMA in this population is also reported. METHODS: To study the frequency of deletions of SMN and NAIP genes in an Iranian sample group, 75 unrelated SMA patients (54 type I, eight type II and 13 type III) were analyzed according to the methods described by van der Steege et al and Roy et al. RESULTS: Homozygous deletion of SMN1 exons 7 and/or 8 were identified in 68 out of 75 patients (90%). Deletion of exon 5 of the NAIP gene was found in 40/54 of type I, 2/8 of type II and 1/13 of type III patients. CONCLUSIONS: Deletion of the SMN1 gene is a major cause of SMA in Iran, and NAIP gene deletions were common in the present patients with type I SMA. Also, the incidence of NAIP deletion is higher in more severe SMA.