Bayesian Survival Analysis of High-Dimensional Microarray Data for Mantle Cell Lymphoma Patients

Moslemi, Azam,Mahjub, Hossein,Saidijam, Massoud,Poorolajal, Jalal,Soltanian, Ali Reza Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.1

Background: Survival time of lymphoma patients can be estimated with the help of microarray technology. In this study, with the use of iterative Bayesian Model Averaging (BMA) method, survival time of Mantle Cell Lymphoma patients (MCL) was estimated and in reference to the findings, patients were divided into two high-risk and low-risk groups. Materials and Methods: In this study, gene expression data of MCL patients were used in order to select a subset of genes for survival analysis with microarray data, using the iterative BMA method. To evaluate the performance of the method, patients were divided into high-risk and low-risk based on their scores. Performance prediction was investigated using the log-rank test. The bioconductor package "iterativeBMAsurv" was applied with R statistical software for classification and survival analysis. Results: In this study, 25 genes associated with survival for MCL patients were identified across 132 selected models. The maximum likelihood estimate coefficients of the selected genes and the posterior probabilities of the selected models were obtained from training data. Using this method, patients could be separated into high-risk and low-risk groups with high significance (p<0.001). Conclusions: The iterative BMA algorithm has high precision and ability for survival analysis. This method is capable of identifying a few predictive variables associated with survival, among many variables in a set of microarray data. Therefore, it can be used as a low-cost diagnostic tool in clinical research.

Peroxisome Proliferator-Activated Receptor-γ Gene Expression and Its Association with Oxidative Stress in Patients with Metabolic Syndrome

Mehdi Hatami,Massoud Saidijam,Reza Yadegarzari,Shiva Borzuei,Alireza Soltanian,Marzieh Safi Arian,Mohammad Taghi Goodarzi 전남대학교 의과학연구소 2016 전남의대학술지 Vol.52 No.3

Regulation of the peroxisome proliferator-activated receptor-γ (PPAR-γ) gene plays an important role in controlling the metabolism of lipids and inflammatory processes. Therefore, it can be associated with the pathogenesis of metabolic syndrome (MetS). The purpose of this study was to determine the expression of this gene in peripheral blood mononuclear cells (PBMC) in patients with metabolic syndrome. Using real-time polymerase chain reaction (PCR), mRNA expression of PPAR-γ was found in PBMC from 37 subjects with MetS and 30 healthy controls. Serum levels of glucose and lipid profiles were measured. The total antioxidant capacity (TAC) was measured using the ferric reducing ability of plasma (FRAP) test. Malondialdehyde (MDA) was determined using a fluorimetric method. Total oxidant status (TOS) in serum was assayed according to oxidation of ferric to ferrous in the presence of methyl orange. Super oxide dismutase (SOD) activity was measured using a Randox kit. Expression of PPAR-γ gene was significantly increased in patients with MetS compared to the control subjects (p=0.002). There was no difference in serum levels of TAC, MDA and SOD between the two study groups, but a significant difference was observed in the TOS (p=0.03). Serum levels of triglycerides and glucose were significantly higher in subjects with MetS. According to the results of our study, an increase in the expression of PPAR-γ in subjects with MetS indicated a possible role of PPAR-γ in the pathogenesis of this disease.

Circulating Betatrophin Levels Are Associated with the Lipid Profile in Type 2 Diabetes

Hassan Ghasemi,Heidar Tavilani,Iraj Khodadadi,Massoud Saidijam,Jamshid Karimi 전남대학교 의과학연구소 2015 전남의대학술지 Vol.51 No.3

Betatrophin is a newly characterized circulating hormone that is produced in tissuessuch as adipose tissue and liver and stimulates pancreatic beta-cell proliferation. Thepurpose of the current study was to examine circulating betatrophin levels in Iranianpatients with type 2 diabetes mellitus (T2DM) and in normal controls. Seventy-five subjectswere enrolled in this case-control study in the following two groups: T2DM patients(n=40) and a group of age-, sex-, and BMI-matched normal control subjects (n=35). Circulating betatrophin concentrations as well as the blood lipid profile, body mass index(BMI), fasting blood sugar (FBS), glycated hemoglobin (HbA1c), and insulin resistancewere determined. Circulating betatrophin levels were significantly higher in patientswith T2DM than in the normal subjects (4.79±1.53 ng/mL vs. 2.79±1.11 ng/mLrespectively; p=0.001). Serum triacylglycerol and total cholesterol were also significantlyhigher in patients with T2DM than in the control group. In the patients withT2DM, serum betatrophin was positively correlated with age, FBS, TG, total cholesterol,and HbA1c. The results of this initial study in Iran have shown that circulating betatrophinlevels are significantly increased in Iranian patients with T2DM comparedwith a control group. Additionally, it is postulated that betatrophin as a novel hormonemay be involved in the generation of an atherogenic lipid profile.

MicroRNA-183 Family in Inner Ear: Hair Cell Development and Deafness

Mohammad Reza Mahmoodian sani,Morteza Hashemzadeh Chaleshtori,Massoud Saidijam,Mohammad-Saeid Jami,Payam Ghasemi-Dehkordi 대한청각학회 2016 Journal of Audiology & Otology Vol.20 No.3

miRNAs are essential factors of an extensively conserved post-transcriptional process controlling gene expression at mRNA level. Varoius biological processes such as growth and differentiation are regulated by miRNAs. Web of Science and PubMed databases were searched using the Endnote software for the publications about the role miRNA-183 family in inner ear: hair cell development and deafness published from 2000 to 2016. A triplet of these miRNAs particularly the miR-183 family is highly expressed in vertebrate hair cells, as with some of the peripheral neurosensory cells. Point mutations in one member of this family, miR-96, underlie DFNA50 autosomal deafness in humans and lead to abnormal hair cell development and survival in mice. In zebrafish, overexpression of the miR-183 family induces extra and ectopic hair cells, while knockdown decreases the number of hair cell. The miR-183 family (miR-183, miR-96 and miR-182) is expressed abundantly in some types of sensory cell in the eye, nose and inner ear. In the inner ear, mechanosensory hair cells have a robust expression level. Despite much similarity of these miRs sequences, small differences lead to distinct targeting of messenger RNAs targets. In the near future, miRNAs are likely to be explored as potential therapeutic agents to repair or regenerate hair cells, cell reprogramming and regenerative medicine applications in animal models because they can simultaneously down-regulate dozens or even hundreds of transcripts.

Evaluation of zinc finger E-box binding homeobox 1 and transforming growth factor-beta2 expression in bladder cancer tissue in comparison with healthy adjacent tissue

Ali Mahdavinezhad,Reza Yadegarazari,Seyed Habibollah Mousavi-Bahar,Jalal Poorolajal,Mohammad Jafari,Mohammad Ali Amirzargar,Hosein Effatpanah,Massoud Saidijam 대한비뇨의학회 2017 Investigative and Clinical Urology Vol.58 No.2

Purpose: The fifth most common cancer is allocated to bladder cancer (BC) worldwide. Understanding the molecular mechanisms of BC invasion and metastasis to identify target therapeutic strategies will improve disease survival. So the aim of this study was to measure expression rate of zinc finger E-box binding homeobox 1 (ZEB1) and transforming growth factor-beta2 (TGF-β2) mRNA in tissue samples of patients with BC and its healthy adjacent tissue samples and their association with muscle invasion, size and grade of the tumor. Materials and Methods: Tissue samples were collected from 35 newly diagnosed untreated patients with BC from 2013 to 2014. Total RNA was extracted from about 50-mg tissue samples using TRIzol reagent. TAKARA SYBR Premix EX Tag II was applied to determine the rate of mRNA expression by real-time polymerase chain reaction (PCR). To obtain final validation, PCR product of ZEB1 and TGF-β2 were sequenced. STATA 11 software was used to analyze the data. Results: The expression level of ZEB1 in tumor samples was significantly more than of in healthy adjacent tissue samples. Up-regulation of TGF-β2 showed a strong association with muscle invasion (p=0.017). There was also demonstrated a relationship between over expression of ZEB1 with the tumor size (p=0.050). Conclusions: It looks ZEB1 and TGF-β2 had a role in BC patients. In this study ZEB1 expression was higher in BC tissues than that of in healthy control tissues. There was demonstrated a markedly association between overexpression of TGF-β2 and muscle invasion. Therefore, they are supposed to be candidate as potential biomarkers for early detection and progression of BC.