Knowledge and Attitude of Infertile People toward Assisted Reproductive Techniques in Hamadan, Iran.

Background: People's knowledge and attitude play a role in deciding whether or not to use assisted reproductive procedures (ART). There is no information about people's attitudes and awareness about ART in western Iran. Thus, this study was performed to determine the knowledge and attitude of infertile people toward ART. Methods: This cross-sectional study was performed on 124 infertile participants who referred to the in vitro fertilization section of Fatemieh hospital, Hamadan, Iran. To measure the knowledge and attitude of the participants, 2 researcher-made questionnaires were used. Their validity and reliability were confirmed by content validity (eg, content validity index [CVI]; content validity ratio [CVR] ) and the Cronbach alpha, respectively. Results: The study involved 124 participants, more than half of whom were women (54.8%). The mean of the CVI and the CVR for the attitude questionnaire was 0.76 and 0.79, respectively, and for the knowledge, questionnaire was 0.72 and 0.71, respectively. The Cronbach alpha coefficient obtained for the attitude and knowledge questionnaires was 0.761 and 0.745, respectively. The mean (SD) of the attitude and knowledge of infertile people toward the use of ART was 15.33 ± 2.91 and 9.04 ± 2.92, respectively. The study reported that participants' age, inhabitation, and job status had a significant effect on their attitude score. Also, the study found that the knowledge score was inversely related to age. The knowledge in those who were unemployed and living in the rural and less than those employed and living in urban areas, respectively. Conclusion: The 2 questionnaires designed in this study (knowledge and attitude) have the required validity and reliability. As a result, it appears that increasing people's knowledge and improving their attitude, particularly among the elderly, is necessary.

Cancer Chemopreventive Activities of Silibinin on Colorectal Cancer through Regulation of E-Cadherin/ß-Catenin Pathway.

PURPOSE: Silibinin is the most active flavonolignan constituent of Silymarin, the extract of milk thistle seeds. In this study, we investigated the anticancer properties and molecular mechanisms of silibinin on colorectal cancer (CRC) cells. METHODS: HCT-116 cells were used to investigate the effects of silibinin on proliferation, migration, epithelial-mesenchymal transition (EMT), cancer stem cells (CSCs), apoptosis and signaling pathways underlying these functions by using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and colony formation assay, quantitative reverse-transcription polymerase chain reaction (RT-qPCR), Western blot, Acridine orange/propidium iodide double staining, migration and sphere formation assay. RESULTS: Silibinin significantly suppressed HCT-116 cells proliferation and migration and induced the apoptosis via increasing the Bax/Bcl-2 ratio. Silibinin down-regulated cancer stemness markers; prominin-1 (CD133), CD44, BMI1, Aldehyde dehydrogenase 1 (ALDH1), and doublecortin-like kinase 1 (DCLK1) of HCT-116 cell line. Silibinin attenuated EMT through decreased expression of N- cadherin and vimentin and increased expression of (E-cadherin). Furthermore, silibinin decreased the ß-catenin gene and protein expression. CONCLUSION: Our study revealed that silibinin maintains various antitumor activities such as induction of apoptosis, suppression of migration, elimination of CSCs and attenuation of EMT related markers in CRC cells. These underlying anti-tumor mechanisms of silibinin are likely to act through the blockage of the ß-catenin signaling pathway, which is the key component of Wnt signaling pathway, one of the hallmarks of CRC development.

Assessment of lncRNA DANCR, miR-145-5p and NRAS axis as biomarkers for the diagnosis of colorectal cancer.

Recent evidence reveals that miRNA sponges neutralize miRNAs activity by binding to miRNAs and sequester them from their relevant targets to regulate expression. The detailed mechanisms of sponge RNAs in colorectal cancer remain to be exactly determined. In this study DANCR, miR-145-5p, NRAS axis was evaluated and the diagnostic value of these targets was assessed in colorectal cancer patients. A case-control study was carried out on 40 samples of tumor tissues and 40 adjacent tissues. Total RNA was extracted, and then, the expression level of DANCR, miR-145-5p and NRAS was evaluated using qRT-PCR. In addition, the sensitivity and specificity of these markers were evaluated by receiver operating characteristic (ROC) curve analysis. Our results revealed that the expression level of DANCR was significantly upregulated in colorectal cancer tissues (p < 0.001). It was demonstrated that DANCR could regulate NRAS expression by sponging miR-145-5 in colorectal cancer patients. Furthermore, the mean expression of miR-145-5p (p < 0.001) and NRAS (p < 0.001) was significantly different between tumor and normal tissue. A significant correlation was observed between DANCR and miR-145-5p (p = 0.001), and also between miR-145-5p and NRAS (p < 0.001). Sensitivity and specificity value for DANCR, miR-145-5p and NRAS were (0.875 and 0.725), (0.875 and 0.745), and (0.877 and 0.694), respectively. According to the values of sensitivities and specificity of DANCR, miR-145-5p and NRAS, confirmed with ROC curve analysis, these biomarkers may be useful in the screening and differentiating between tumor and control sample in colorectal neoplasm.

Novel MYO15A variants are associated with hearing loss in the two Iranian pedigrees.

BACKGROUND: Clinical genetic diagnosis of non-syndromic hearing loss (NSHL) is quite challenging. With regard to its high heterogeneity as well as large size of some genes, it is also really difficult to detect causative mutations using traditional approaches. One of the recent technologies called whole-exome sequencing (WES) has been thus developed in this domain to remove the limitations of conventional methods. METHODS: This study was a report on a research study of two unrelated pedigrees with multiple affected cases of hearing loss (HL). Accordingly, clinical evaluations and genetic analysis were performed in both families. RESULTS: The results of WES data analysis to uncover autosomal recessive non-syndromic hearing loss (ARNSHL) disease-causing variants was reported in the present study. Initial analysis identified two novel variants of MYO15A i.e. c.T6442A:p.W2148R and c.10504dupT:p.C3502Lfs*15 correspondingly which were later confirmed by Sanger validations and segregation analyses. According to online prediction tools, both identified variants seemed to have damaging effects. CONCLUSION: In this study, whole exome sequencing were used as a first approach strategy to identify the two novel variants in MYO15A in two Iranian families with ARNSHL.

Anticancer effects of miR-200c in colorectal cancer through BMI1.

Colorectal cancer (CRC) is one of the most leading cancer deaths throughout the world. MiR-200c has been shown to have a critical role in cancer initiation and progression. In this study, we investigated the miR-200c expression in CRC tissues and its effects on CRC cell lines which were mediated by polycomb complex protein (BMI1). Quantitative reverse transcription polymerase chain reaction (QRT-PCR) and immunohistochemistry were used to detect miR-200c and BMI1 expression in tumor tissues from 38 patients with CRC and 38 normal colon tissues. HCT-116 and SW-48 cells were transfected by locked nucleic acid (LNA)-anti-miR-200c. Western blot analysis and real-time PCR were applied to determine the BMI1 protein and microRNA (miRNA) levels. The apoptosis was analyzed via annexin/propidium iodide staining, and cell invasion was evaluated by transwell assay. MiR-200c was markedly downregulated in CRC tissues, whereas the protein expression of BMI1 in CRC tissues was upregulated compared with normal colon tissues. In the colon cancer cell lines, transfection of LNA-anti-miR-200c increased BMI1 gene and protein expression as well as the cell invasion. Downregulation of miR-200c by LNA decreased the apoptotic cells. The results from this study revealed that miR-200c may have antitumor effects through inhibition of BMI1 expression.

The Performance Evaluation of The Random Forest Algorithm for A Gene Selection in Identifying Genes Associated with Resectable Pancreatic Cancer in Microarray Dataset: A Retrospective Study.

OBJECTIVE: In microarray datasets, hundreds and thousands of genes are measured in a small number of samples, and sometimes due to problems that occur during the experiment, the expression value of some genes is recorded as missing. It is a difficult task to determine the genes that cause disease or cancer from a large number of genes. This study aimed to find effective genes in pancreatic cancer (PC). First, the K-nearest neighbor (KNN) imputation method was used to solve the problem of missing values (MVs) of gene expression. Then, the random forest algorithm was used to identify the genes associated with PC. MATERIALS AND METHODS: In this retrospective study, 24 samples from the GSE14245 dataset were examined. Twelve samples were from patients with PC, and 12 samples were from healthy control. After preprocessing and applying the fold-change technique, 29482 genes were used. We used the KNN imputation method to impute when a particular gene had MVs. Then, the genes most strongly associated with PC were selected using the random forest algorithm. We classified the dataset using support vector machine (SVM) and naïve bayes (NB) classifiers, and F-score and Jaccard indices were reported. RESULTS: Out of the 29482 genes, 1185 genes with fold-changes greater than 3 were selected. After selecting the most associated genes, 21 genes with the most important value were identified. S100P and GPX3 had the highest and lowest importance values, respectively. The F-score and Jaccard value of the SVM and NB classifiers were 95.5, 93, 92, and 92 percent, respectively. CONCLUSION: This study is based on the application of the fold change technique, imputation method, and random forest algorithm and could find the most associated genes that were not identified in many studies. We therefore suggest researchers use the random forest algorithm to detect the related genes within the disease of interest.

Identification of key genes in colorectal cancer diagnosis by co-expression analysis weighted gene co-expression network analysis.

BACKGROUND: The purpose of this study was using bioinformatics tools to identify biomarkers and molecular factors involved in the diagnosis of colorectal cancer, which are effective for the diagnosis and treatment of the disease. METHODS: We determined differentially expressed genes (DEGs) related to colorectal cancer (CRC) using the data series retrieved from GEO database. Then the weighted gene co-expression network analysis (WGCNA) was conducted to explore co-expression modules related to CRC diagnosis. Next, the relationship between the integrated modules with clinical features such as the stage of CRC was evaluated. Other downstream analyses were performed on selected module genes. RESULTS: In this study, after performing the WGCNA method, a module named blue module which was more significantly associated with the CRC stage was selected for further evaluation. Afterward, the Protein-protein interaction network through sting software for 154 genes of the blue module was constructed and eight hub genes were identified through the evaluation of constructed network with Cytoscape. Among these eight hub genes, upregulation of MMP9, SERPINH1, COL1A2, COL5A2, COL1A1, SPARC, and COL5A1 in CRC was validated in other microarray and TCGA data. Based on the results of the mRNA-miRNA interaction network, SERPINH1 was found as a target gene of miR-940. Finally, results of the DGIDB database indicated that Andecaliximab, Carboxylated glucosamine, Marimastat, Tozuleristide, S-3304, Incyclinide, Curcumin, Prinomastat, Demethylwedelolactone, and Bevacizumab, could be used as a therapeutic agent for targeting the MMP9. Furthermore, Ocriplasmin and Collagenase clostridium histolyticum could target COL1A1, COL1A2, COL5A1, and COL5A2. CONCLUSION: Taken together, the results of the current study indicated that seven hub genes including COL1A2, COL5A1, COL5A2, SERPINH1, MMP9, SPARC, and COL1A1 which were upregulated in CRC could be used as a diagnostic and progression biomarker of CRC. On the other hand, miR-940 which targets SERPINH1 could be used as a potential biomarker of CRC. More ever, Andecaliximab, Carboxylated glucosamine, Marimastat, Tozuleristide, S-3304, Incyclinide, Curcumin, Prinomastat, Demethylwedelolactone, Bevacizumab, Ocriplasmin , and Collagenase clostridium histolyticum were introduced as therapeutic agents for CRC which their therapeutic potential should be evaluated experimentally.

Anticancer Effects of Gold Nanoparticles by Inducing Apoptosis in Bladder Cancer 5637 Cells.

Nanotechnology is a developing and revolutionary science that has been widely recommended for diagnosis and treatment of cancer. Among the various nanoparticles used in nanotechnology, gold nanoparticles (AuNPs) have attracted much attentions due to their promising anticancer properties. Despite the potential advantages of AuNPs, their apoptotic and anti-angiogenic effects have not yet been reported on human bladder cancer 5637 cells. This motivated us to evaluate (reactive oxygen species) ROS-mediated apoptosis in 5637 cells. For this task, inhibitory effect of AuNPs was investigated after 24-h exposure to different concentrations of AuNPs by MTT assay. Also, apoptosis level was assessed by ROS production, flow cytometry, and Hoechst 33,258 staining. Besides, mRNA expression of B-cell lymphoma protein 2 (Bcl-2), Bcl-2-associated X (Bax), vascular endothelial growth factor A (VEGFA) genes, and caspase-3,7 activity were determined by qRT-PCR and colorimetric assay, respectively. Moreover, migration rate was evaluated by wound healing assay. MTT results demonstrate that AuNPs can reduce 5637-cell viability in a dose-dependent manner, while fluorimetric assay data show significant increased ROS production in 25 and 50 µg/ml-treated cells. It is also observed that AuNPs lead to Bax overexpression and downregulation of Bcl-2 and VEGFA genes. In line with this, flow cytometry results show increased levels of apoptosis in 25 and 50 µg/ml AuNP-treated cells (p < 0.05). Similarly, Hoechst staining indicates a remarkable increase in cells with apoptotic morphology after treating with AuNPs. Overall, our findings show that AuNPs significantly provoke ROS production, induce apoptosis, and suppress cell migration in bladder cancer 5637 cells.

Effects of gold nanoparticles on oxidative stress status in bladder cancer 5637 cells.

INTRODUCTION: Nanomedicine has recently been known as an emerging research area with promising applications in cancer diagnosis and treatment. Aside from this, gold nanoparticles (AuNPs), as one of the important components of nanomedicine, have attracted considerable attention due to their special physicochemical properties and lower toxicity than other nanoparticles. Despite the impressive advantages of AuNPs, it has not been yet determined whether oxidative stress contributes to the toxicity of AuNPs on bladder cancer. AIM: The aim of this study was to address this issue by conducting experiments in order to investigate the effects of 20 nm AuNPs on human bladder cancer 5637 cells. MATERIALS AND METHODS: The viability of 5637 cells was evaluated upon 24 hour exposure to different concentrations of AuNPs (0- 50 µg/ml) by 3-(4, 5-dimethylthiazol, 2-yl)-2, 5-diphenyl tetrazolium bromide (MTT) assay. In order to evaluate oxidative stress status, total antioxidant capacity (TAC), total oxidant status (TOS), malondialdehyde (MDA) and also activities of antioxidant enzymes including glutathione peroxidase (GPx), catalase (CAT) and superoxide dismutase (SOD) were all determined by colorimetric assay kits. RESULTS: The results from our experiment showed that the cytotoxicity caused by AuNPs was dose-dependent and the IC50 value was found to be 43.14 µg/ml after 24-hour exposure. Furthermore, MDA and TOS levels were significantly increased in treated cells compared to untreated cells (p.

Identification of Risk Factors for COVID-19-related Death using Machine Learning Methods.

Background: Unknown cases of pneumonia appeared in late 2019 in Wuhan, China. Following the worldwide spread of the disease, the World Health Organization declared it a pandemic on March 11, 2020. The total number of infected people worldwide as of December 16, 2020, was more than 74 million, more than one million and six hundred thousand of whom died from Coronavirus Disease 2019 (COVID-19). This study aimed to identify the risk factors for the mortality of COVID-19 in Hamadan, west of Iran. Materials and Methods: This cross-sectional study used the information of all patients with COVID-19 admitted to Shahid Beheshti and Sina hospitals in Hamadan during January 2020-November 2020. Logistic regression model, decision tree, and random forest were used to assess risk factors for death due to COVID-19. Results: This study was conducted on 1853 people with COVID-19. Blood urea nitrogen change, SPO2 at admission, the duration of hospitalization, age, neutrophil count, lymphocyte count, number of breaths, complete blood count, systolic blood pressure, hemoglobin, and sodium were effective predictors in both methods of decision tree and random forest. Conclusion: The risk factors identified in the present study may serve as surrogate indicators to identify the risk of death due to COVID-19. The proper model to predict COVID-19-related mortality is random forest based on sensitivity.

The Effect of miR-145-5p, DANCR and NRAS Expression Levels on the Survival Rate of Colorectal Cancer Patients.

BACKGROUND: The prevalence of colorectal cancer (CRC) has been increasing in the world. There are different factors for colorectal cancer, and changes in the levels of gene expression such as miR-145-5p, DANCR and NRAS can be one of the factors. METHODS: The case-control study was performed on 40 CRC specimens and 40 adjacent healthy tissues. Fresh tumor and tumor-free adjacent tissue samples were obtained from patients who underwent the surgical operation as a conventional treatment procedure. After tumor resection, the specimens were immediately frozen in liquid nitrogen and stored at -80°C until further investigation. Cox regression was used to get the hazard ratios. RESULTS: The mean ± SD age of the patients was 62.45± 12.89 years. Of these, 62.5% were males. The risk of death from CRC in patients with low miR-145-5p levels is about 10 times higher than the high expression levels (HR = 10.759, P = 0.009). High expression levels of NRAS can increase the risk of CRC death up to 4 times (HR = 4.12, P = 0.045). The study did not show a relationship between DANCR expression levels and death risk from CRC (HR = 1.582, P = 0.439). CONCLUSION: These expression levels revealed that miRNA-145-5p and NRAS can be utilized as diagnostic biomarkers in colorectal cancer death. This may also introduce the microRNAs as colorectal cancer therapeutic targets.

Predictors of COVID-19 related death in diabetes patients: A case-control study in Iran.

BACKGROUND: Identifying the predictors of COVID-19 related death in diabetes patients can assist physicians for detecting risk factors related to the worse outcome in these patients. In this study we investigated the predictors of the death in patients with diabetes compared with non-diabetic COVID-19 patients. METHODS: In the present case-control study, the case group were diabetic patients with COVID-19 and the control group included Non-diabetic COVID-19 patients. The data source regarding the demographic characteristics, clinical symptoms, laboratory, and radiological findings on admission as well as the complications, treatment, and outcomes during hospitalization were gathered from their medical record through two trained nurses. Adjusted and unadjusted odds ratios (OR) estimate were calculated using the simple and multiple logistic regression through backward model. RESULTS: The mean (SD) age of the case group was higher than that of the control group; [65.24 (12.40) years vs. 59.35 (17.34) years, respectively (P < 0.001)]. Results of the adjusted logistic regression model showed that, advanced age (+60 year) (OR = 5.13, P = 0.006), addiction (OR = 5.26, P = 0.033), high level of Blood urea nitrogen (OR = 5.85, P < 0.001), and high level of Alkaline Phosphatase (OR = 3.38, P = 0.012) in diabetic patients were significantly associated with increase the odds of death in COVID-19 patients. CONCLUSION: We found that in COVID-19 patients with diabetes; advanced age, addiction, high level of BUN and Alp and in non-diabetic COVID-19 patients advanced age, dyspnea, high level of BUN and SGOT were associated with increase risk of death in these patients.

Association between rs11614913 Polymorphism of The MiR-196-a2 Gene and Colorectal Cancer in The Presence of Departure from Hardy-Weinberg Equilibrium.

OBJECTIVE: Colorectal cancer (CRC) is the fourth most common and the second most lethal cancer worldwide. CRC mortality is increasing in Iran. In the current study, we aimed to investigate association between rs11614913 polymorphism of the miR-196-a2 gene and CRC. MATERIALS AND METHODS: In this case-control study, we assessed association of the rs11614913 polymorphism in 194 patients with CRC (case) and 286 healthy individuals (control). The expectation-maximization (EM) algorithm method was used to adjust deviation from Hardy-Weinberg equilibrium (HWE). RESULTS: There was no significant difference between genotypic frequencies of rs11614913 polymorphism in the control and case groups. Genotypic frequencies differed in the adjusted and unadjusted deviations from the HWE. Analysis of unadjusted and adjusted independent variables showed that age, sex, alcohol consumption, and drug use were statistically significant. CONCLUSION: Our findings showed that rs11614913 polymorphism was not associated with CRC risk. Deviation from HWE affected the results. It is recommended to perform further studies to establish HWE. Ignoring the equilibrium can cause in consistencies in the results of studies.

DCLK1 Inhibition Sensitizes Colorectal Cancer Cells to Radiation Treatment.

Colorectal cancer (CRC) is one of the most prevalent diagnosed cancers and a common cause of cancer-related mortality. Despite effective clinical responses, a large proportion of patients undergo resistance to radiation therapy. Therefore, the identification of efficient targeted therapy strategies would be beneficial to overcome cancer radioresistance. Doublecortin-like kinase 1 (DCLK1) is an intestinal and pancreatic stem cell marker that showed overexpression in a variety of cancers. The transfection of DCLK1 siRNA to normal HCT-116 cells was performed, and then cells were irradiated with X-rays. The effects of DCLK1 inhibition on cell survival, apoptosis, cell cycle, DNA damage response (ATM and γH2AX proteins), epithelial-mesenchymal transition (EMT) related genes (vimentin, N-cadherin, and E-cadherin), cancer stem cells markers (CD44, CD133, ALDH1, and BMI1), and ß-catenin signaling pathway (ß-catenin) were evaluated. DCLK1 siRNA downregulated DCLK1 expression in HCT-116 cells at both mRNA and protein levels (P <0.01). Colony formation assay showed a significantly reduced cell survival in the DCLK1 siRNA transfected group in comparison with the control group following exposure to 4 and 6 Gy doses of irradiation (P <0.01). Moreover, the expression of cancer stem cells markers (P <0.01), EMT related genes (P <0.01), and DNA repair proteins including pATM (P <0.01) and γH2AX (P <0.001) were significantly decreased in the transfected cells in comparison with the nontransfected group after radiation. Finally, the cell apoptosis rate (P <0.01) and the number of cells in the G0/G1 phase in the silencing DCLK1 group was increased (P <0.01). These findings suggest that DCLK1 can be considered a promising therapeutic target for the treatment of radioresistant human CRC.

Assessing the Reliability and Validity of the Persian Version of the Chronic Pelvic Pain Questionnaire in Women.

PURPOSE: There is a need for developing a standard and approved tool to assess chronic pelvic pain (CPP) in Iranian women. The aim of this study was to investigate the reliability and validity of the Persian version of the pelvic pain and urinary/frequency (PUF) questionnaire in Iranian women with CPP. MATERIALS AND METHODS: This cross-sectional study was performed on 50 females with CPP referred to the urology clinic of Kerman University of Medical Sciences from 2018 to 2019. Initially, the PUF questionnaire was translated into Persian and then back translated into English. The face validity of the tool was evaluated by being tested on 50 patients who had different literacy levels to ensure its understandability and acceptability by patients. The construct validity was evaluated through both exploratory and confirmatory factor analyses. The internal consistency was also analyzed by determining Cronbach's alpha coefficient and test-retest method. RESULTS: The Persian version of the questionnaire was compatible with the original English version. The Kisser sampling adequacy index was calculated on the data before extracting the factors indicating good factor accessibility of the questionnaire statements. The construct validity of the questionnaire was confirmed using exploratory and confirmatory factor analyses. The internal consistency parameters were also acceptable. Cronbach's alpha coefficient of the whole questionnaire, as well as the coefficients of the "signs/symptoms" and "unpleasant feelings" domains were 77%, 74%, and 78%, respectively. CONCLUSION: The developed Persian version of the PUF questionnaire retrieved a good validity and reliability.

Reducing False Negative PCR Test for COVID-19.

As the SARS-CoV-2 (COVID-19) pandemic spreads rapidly, there is need for a diagnostic test with high accuracy to detect infected individuals especially those without symptoms. Real-time polymerase chain reaction (RT-PCR) is a common molecular test for diagnosing SARS-CoV-2. If some factors are not taken into consideration when performing this test, it can have a relatively large number of false negative results. In this article, we discuss important considerations that could lead to false negative test reduction.

A Bayesian analysis for investigating the association between rs13266634 polymorphism in SLC30A8 gene and type 2 diabetes.

PURPOSE: The purpose of this study was to evaluate the association between rs13266634 polymorphism in SLC30A8 gene and type 2 diabetes in Iranian population, and also to provide a way for adjusting the deviation from the Hardy-Weinberg equilibrium. METHODS: This was a case-control study, the patients were selected from the East Azerbaijan province, Iran. In this study, 125 patients with type 2 diabetes (cases) and 125 healthy individuals (controls) were studied. Genotype and allele frequencies were determined in both groups, and the deviations from the Hardy-Weinberg equilibrium were assessed using Bayesian analysis. RESULTS: A statistically significant association was observed between rs13266634 polymorphism in SLC30A8 gene and type 2 diabetes. In genotype assessing, data analysis showed that, TT genotype play a role in diabetes type 2 risk (P = 0.001). Subjects with TT genotype had a lower risk of diabetes compared to those with CC and CT genotypes. Also, there was no significant relationship between this polymorphism and type 2 diabetes mellitus in the absence of Hardy-Weinberg equilibrium. CONCLUSION: Our findings show that, rs13266634 polymorphism was associated with the type 2 diabetes risk in the population of Eastern Azerbaijan province; however, the low number of TT homozygous genotypes affected the precision of the results. Also, the deviation from HWE affected the results. It is recommended to perform further studies to establish Hardy-Weinberg equilibrium. The inconsistency in the results may be due to the ignorance of this equilibrium.

Identification of A Gene Set Associated with Colorectal Cancer in Microarray Data Using The Entropy Method.

OBJECTIVE: We sought to apply Shannon's entropy to determine colorectal cancer genes in a microarray dataset. MATERIALS AND METHODS: In the retrospective study, 36 samples were analysed, 18 colorectal carcinoma and 18 paired normal tissue samples. After identification of the gene fold-changes, we used the entropy theory to identify an effective gene set. These genes were subsequently categorised into homogenous clusters. RESULTS: We assessed 36 tissue samples. The entropy theory was used to select a set of 29 genes from 3128 genes that had fold-changes greater than one, which provided the most information on colorectal cancer. This study shows that all genes fall into a cluster, except for the R08183 gene. CONCLUSION: This study has identified several genes associated with colon cancer using the entropy method, which were not detected by custom methods. Therefore, we suggest that the entropy theory should be used to identify genes associated with cancers in a microarray dataset.

Diagnostic Value of Plasma Long Non-coding RNA HOTTIP as a Non-invasive Biomarker for Colorectal Cancer (A Case- Control Study).

Long non-coding RNAs (lncRNAs), associated with various cancers including colorectal cancer (CRC), could be collected from body fluids easily. Our aims were to determine the expression level of HOTTIP lncRNA in plasma samples of healthy individuals and CRC patients as well as their relationship with clinico-pathological characteristics of patients. First, total RNA was extracted from the plasma samples of 100 subjects including 50 patients and 50 age and sex matched healthy persons. Then, gene expression was measured using real-time PCR technique. The sensitivity and specificity of HOTTIP dysregulation in CRC and healthy individual's plasma was measured by receiver operating characteristic (ROC) analysis. As compared with healthy controls, HOTTIP lncRNA was over expressed in a statistically significant manner in plasma samples of patients (P=0.001). Significant relationship between HOTTIP expression and positive family history of CRC was observed, too (P=0.04). The ROC curve analysis showed an AUC value of 0.775, a specificity of 82%, a sensitivity of 76%, with a cut off value equal to 2.40 (P =0.001). HOTTIP transcript can be proposed as a new biomarker for early diagnosis due to the increased expression in plasma samples of patients with CRC and the relatively high sensitivity and specificity.

Mitochondrial Variants in Pompe Disease: A Comparison between Classic and Non-Classic Forms.

OBJECTIVE: Pompe disease (PD) is a progressive neuromuscular disorder that is caused by glucosidase acid alpha (GAA) deleterious mutations. Mitochondrial involvement is an important contributor to neuromuscular diseases. In this study the sequence of MT-ATP 6/8 and Cytochrome C oxidase I/II genes along with the expression levels of the former genes were compared in classic and non-classic patients. MATERIALS AND METHODS: In this case-control study, the sequence of MT-ATP 6/8 and Cytochrome C oxidase was analyzed by polymerase chain reaction (PCR)-Sanger sequencing and expression of MT-ATP genes were quantified by real time-PCR (RT-PCR) in 28 Pompe patients. The results were then compared with 100 controls. All sequences were compared with the revised Cambridge reference sequence as reference. RESULTS: Screening of MT-ATP6/8 resulted in the identification of three novel variants, namely T9117A, A8456C and A8524C. There was a significant decrease in MT-ATP6 expression between classic (i.e. adult) and control groups (P=0.030). Additionally, the MT-ATP8 expression was significantly decreased in classic (P=0.004) and non-classic (i.e. infant) patients (P=0.013). In total, 22 variants were observed in Cytochrome C oxidase, five of which were nonsynonymous, one leading to a stop codon and another (C9227G) being a novel heteroplasmic variant. The A8302G in the lysine tRNA gene was found in two brothers in a pedigree, while a T7572C variant in the aspartate tRNA gene was observed in two brothers in another pedigree. CONCLUSION: The extent of mitochondrial involvement in the classic group was more significant than in the non-classic form. Beside GAA deleterious mutations, it seems that mtDNA variants have a secondary effect on PD. Understanding, the role of mitochondria in the pathogenesis of Pompe may potentially be helpful in developing new therapeutic strategies.