Neurofibromatosis-Noonan syndrome and growth deficiency in an Iranian girl due to a pathogenic variant in NF1 gene.

BACKGROUND: Mutations in NF1 gene could cause allelic disorders with clinical spectrum of Neurofibromatosis type 1 to Noonan syndrome. Here, a 7-year-old Iranian girl is described with Neurofibromatosis-Noonan syndrome due to a pathogenic variant in NF1 gene. METHODS: Clinical evaluations were performed along with genetic testing using whole exome sequencing (WES). The variant analysis including pathogenicity prediction was also done using bioinformatics tools. RESULTS: The chief compliant of the patient was short stature and lack of proper weight gain. Other symptoms were developmental delay, learning disability, inadequate speech skill, broad forehead, hypertelorism, and epicanthal folds, low set ears and webbed neck. A small deletion, c.4375-4377delGAA, was found in NF1 gene using WES. This variant was classified as pathogenic according to ACMG. CONCLUSIONS: NF1 variants may show variable phenotypes among the patients; identifying such variants is helpful in therapeutic management of the disease. WES is considered as an appropriate test to diagnose Neurofibromatosis-Noonan syndrome.

rs6426881 in the 3'-UTR of PBX1 is involved in breast and gastric cancers via altering the binding potential of miR-522-3p.

BACKGROUND: Breast and gastric cancers are the most important diseases that lead to cancer death and social healthcare challenge. Overexpression of PBX1, a proto-oncogene, is correlated with the progression and metastasis of various cancers. For the first time, in this study the researchers evaluated the relationship between rs6426881, affecting miR-522-3p binding to the PBX1, with breast and gastric cancers. METHODS AND RESULTS: The Microarray analysis was performed for finding the relative expression level of PBX1 and hsa-miR-522-3p, based on high throughput experiments. The GSE54397, GSE112369, GSE10810, GSE241585.ER, GSE24185.PR, GSE68373, and GSE38167 datasets were analyzed. A case-control study was carried out in 123 Iranian suffering from breast cancer and 132 participants as control samples as well as 130 people suffering from gastric cancer and 54 people as control group members. SNP rs6426881 in the 3'-UTR of PBX1 was genotyped by the High-Resolution Melting (HRM) method. Association analysis revealed that rs6426881 is correlated with Estrogen and Progesterone receptors, grade, and stage of breast cancer. Furthermore, a significant relationship was observed between the genotypes and blood groups in gastric cancer, while the distribution of alleles was significantly related to smoking, status of the primary tumor, and metastasis (Chi-Square P < 0.05). Finally, Bioinformatics analyses suggested that rs6426881 contains binding sites for miR-522-3p in the 3'-UTR of PBX1 transcript. The finding suggested that TT genotype is associated with poor prognosis in breast and gastric cancer. CONCLUSIONS: The rs6426881 T allele at PBX1 3'-UT is significantly related to breast and gastric cancers by altering the regulatory affinity of miR-522-3p to PBX1 3'-UTR and may be suggested as a novel prognostic biomarker for the diseases.

The miR526b-5p-Related Single Nucleotide Polymorphisms, rs72618599, Located in 3'-UTR of TCF3 Gene, is Associated with the Risk of Breast and Gastric Cancers

Background: Single nucleotide polymorphisms result in dysregulation of the proto-oncogene TCF3 gene, which is associated with the development, metastasis, and chemoresistance of different malignancies. Methods: GSE10810 microarray dataset and GEPIA2 online software were used to find differentially expressed genes and the TCF3 status in breast cancer (BC) and gastric cancer (GC), respectively. Plots and figures of microarray analysis were prepared by ggplot2 and pheatmap packages. Differentially expressed genes were obtained by the Bioconductor limma package. In silico analysis was used to predict the functions of rs72618599. BC (n = 123), GC (n = 132) and healthy age and gender matched controls (n = 184) were genotyped, using the high-resolution melting technique. Results: Based on the allelic comparison study, C allele of rs72618599 was associated with the BC tumor stage IV (66.1%, 78/120, p < 0.0001) and grade III (52.4%, 55/72, p < 0.0001), while the T allele was associated with metastasis (84.2%, 10/162, p < 0.0001). However, in GC patients, the C allele was significantly correlated with H. pylori infection (51.7%, 30/58, p = 0.008), stage III of primary tumors (47.7%, 62/88, p = 0.017), stage II of lymph node status (35.5%, 44/74, p = 0.017), and metastasis (52.9%, 90/132, p = 0.044). In silico analysis predicted that rs72618599 leads to the creation of a binding site for hsa-miR526b-5p in the 3'-UTR of TCF3 transcript. Conclusion: Regarding the rs72618599 SNP, the C allele, is associated with poor prognosis of BC and GC. Furthermore, rs72618599 may be associated with cancer progression by altering the regulatory affinity of hsa-miR526b-5p to 3'-UTR of TCF3.

Frequency of background and radiation-induced apoptosis in leukocytes of individuals with alpha-thalassemia variants, assessed by the neutral comet assay.

To study effects of ionizing radiation on apoptosis induction in leukocytes of alpha-thalassemia (alpha-thal) variants compared to normal controls, venous blood samples were obtained from 10 healthy volunteers and 30 alpha-thal patients. Different types alpha-thal were diagnosed by multiplex polymerase chain reaction (PCR). Blood samples were irradiated with three Gy gamma rays, used for comet assay, immediately or 48 h after irradiation. Results show that the frequency of background as well as apoptosis in silent alpha-thal carriers, alpha-thal carriers and controls was similar but there was a significant difference between Hb H patients and other groups in the study. The increased apoptosis in Hb H patients might suggest that accumulation of beta-globin and oxidative stresses are effective in causing apoptosis, and cells from these patients are more vulnerable to damage from radiation-induced toxic substances. Therefore, from alpha-thal patients, those with Hb H disease might be considered as radiosensitive in terms of apoptosis formation.

Polymorphism variant of MnSOD A16V and risk of female infertility in northern Iran.

OBJECTIVE: Infertility is a disease of the reproductive system defined by inability to conceive after having regular unprotected intercourse. Both environmental and genetic factors can be involved in female infertility. Manganese superoxide dismutase (MnSOD) is a crucial mitochondrial antioxidant enzyme that has a key role in cellular defense against agents that induce oxidative stress. The present study was aimed to evaluate the MnSOD A16V gene polymorphism in female infertility in northern Iran. MATERIALS AND METHODS: Samples were obtained from 150 patients diagnosed with female infertility and 150 controls and genotyped by the polymerase chain reaction-restriction fragment length polymorphism method. RESULTS: The MnSOD genotype frequencies amongst the 150 cases were A/A = 27.3%, A/V = 69.4%, and V/V = 3.3%; the A and V allele frequencies were 62% and 38%, respectively. The MnSOD genotype frequencies amongst the 150 controls were A/A = 33.3%, A/V = 48.0%, and V/V = 18.7%; the A and V allele were 57% and 43%, respectively. We observed a significant difference in genotype distributions of MnSOD A16V polymorphism between patients and controls (p = 0.0001). CONCLUSION: It is suggested that the MnSOD A16V polymorphism may be associated with a risk of female infertility in northern Iran. More studies should be considered with a larger number of patients and controls to confirm our results.

A low-cost efficient multiplex PCR for prenatal sex determination in bovine fetus using free fetal DNA in maternal plasma.

BACKGROUND: In order to establish a reliable non-invasive method for sex determination in a bovine fetus in a routine setting, the possibility of identifying specific sequence in the fetal X and Y-chromosomes has been evaluated in maternal plasma using conventional multiplex polymerase chain reaction (PCR) analysis. The aim of this study was to provide a rapid and reliable method for sexing bovine fetuses. MATERIALS AND METHODS: In this experimental study, peripheral blood samples were taken from 38 pregnant heifers with 8 to 38 weeks of gestation. DNA template was extracted by phenol-chloroform method from 350 µl maternal plasma. Two primer pairs for bovine amelogenin gene (bAML) and BC1.2 were used to amplify fragments from X and Y chromosomes. A multiplex PCR reaction has been optimized for amplification of 467 bp and 341 bp fragments from X and Y bAML gene and a 190 bp fragment from BC1.2 related to Y chromosome. RESULTS: The 467 bp fragment was observed in all 38 samples. Both 341 and 190 bp fragments were detected only in 24 plasma samples from male calves. The sensitivity and specificity of test were 100% with no false negative or false positive results. CONCLUSION: The results showed that phenol-chloroform method is a simple and suitable method for isolation of fetal DNA in maternal plasma. The multiplex PCR method is an available non-invasive approach which is cost efficient and reliable for sexing bovine fetuses.

Evaluation of two DNA extraction methods from maternal plasma for using in non-invasive bovine fetus gender determination.

BACKGROUND: Fetal DNA in maternal plasma and serum has been shown to be a useful material for prenatal fetal sex determination during early gestational ages. Non-invasive prenatal diagnosis is now possible at 8(th) week of pregnancy, by maternal blood sample testing. OBJECTIVE: The purpose of this study was to evaluate two DNA extraction methods from mother plasma and its routine clinical application in bovine fetus gender determination with non-invasive method. MATERIALS AND METHODS: Maternal blood samples were taken from 40 pregnant cows during the 8(th)-38(th) weeks of gestation. DNA was extracted from 350 µl of maternal plasma with two salting-out and phenol-chloroform methods. The absorption in A260 and purity (A260/A280) of extracted DNA were detected by ultraviolet spectrophotometer. Three µl of the extracted DNA with phenol-chloroform method was used as a template. The PCR reaction was carried out to amplify the fragments of X and Y chromosomes of amelogenin, TSPY and BC1.2 genes. RESULTS: The difference between the mean absorption of DNA extracted by phenol-chloroform method and salting-out method was not significant in A260 (p>0.05, p=0.3549), but the difference between mean purity (A260/A280) of DNA extracted by phenol-chloroform method and salting-out method was significant (p<0.001). X chromosome fragment was detected in all 40 samples and Y chromosome fragments were detected in 25 plasma samples which were delivered a male calf. The sensitivity and specificity of test was 100% with no false negative and false positive results. CONCLUSION: The results showed that phenol-chloroform method is a simple and sensitive method for isolation of fetal DNA in maternal plasma.

The Correlation between Microsatellite Instability and the Features of Sporadic Colorectal Cancer in the North Part of Iran.

Background. The aim of this study was to determine the correlation between MSI and sporadic colorectal cancer in Guilan province, North part of Iran. Materials and Methods. A total of 96 patients who underwent resection for sporadic colorectal cancer in Guilan province were studied. No patients had positive family history of cancers. The frequencies of MSI were analyzed by testing the BAT-26 and BAT-25 markers. Results. MSI analysis revealed that 22.9% of the tumors (22 patients) were microsatellite instability positive and 77.1% (74 patients) were microsatellite instability negative. The highest rate of MSI (40.9%) was found in the rectal region. MSI-H status was seen more frequently in distal tumors (P = 0.04, odds ratio = 3.13, 0.96-10.14). Conclusions. Distal tumor location and MSI may associate with special clinicopathological features. It seems that there may be correlation with underlying genetic and immunologic mechanisms.