جستجوی مقالات مرتبط با کلیدواژه « Gene » در نشریات گروه « پزشکی »

Phosphorylation reactions highlight the essential role of protein kinases in sperm motility. TSSK6 protein is thought to play a crucial role in this process. Indeed, sperm obtained from mice with the Tssk6-/- genotype are unable to carry out fertilization and exhibit decreased motility. This leads us to investigate the causes of asthenozoospermia by searching for polymorphisms in the TSSK6 gene. Therefore, the objective of this study is to identify polymorphisms in the TSSK6 gene in men affected by asthenozoospermia.

The methodology involved direct sequencing of spermatozoa DNA. Thirty ejaculates were analyzed, including 20 from asthenozoospermic men and 10 from normozoospermic men. Spermograms were performed according to WHO procedures. DNA extraction was carried out using the phenol/chloroform method followed by conventional PCR. The amplicons were sequenced using the Sanger method, and the sequences were analyzed with BioEdit software. The data were analyzed using Fisher and Mann-Whitney tests.

The results revealed mutations in the TSSK6 gene in both normospermic and asthenozoospermic ejaculates. The synonymous mutations c.690T>C (p.Tyr230Tyr) and c.372C>A (p.Arg124Arg) were the most frequent, occurring at rates of 50% and 33.33%, respectively. Analysis of the mutations using PolyPhen-2 indicated that all mutations observed in normozoospermic samples are benign and would not affect sperm quality. However, only the mutations described in asthenozoospermic samples are predicted to be damaging to the protein.

 In conclusion, mutations in the TSSK6 gene were observed in infertile men. Deleterious mutations in the TSSK6 protein are associated with asthenozoospermia

This study aimed to introduce a biomarker panel to detect pancreatic ductal adenocarcinoma (PDAC) in the early stage, and also differentiate of stages from each other.

PDAC is a lethal cancer with poor prognosis and overall survival.

Gene expression profiles of PDAC patients were extracted from the Gene Expression Omnibus (GEO) database. The genes that were significantly differentially expressed (DEGs) for Stages I, II, and III in comparison to the healthy controls were identified. The determined DEGs were assessed via protein–protein interaction (PPI) network analysis, and the hub-bottleneck nodes of analyzed networks were introduced.

A number of 140, 874, and 1519 significant DEGs were evaluated via PPI network analysis. A biomarker panel including ALB, CTNNB1, COL1A1, POSTN, LUM, and ANXA2 is presented as a biomarker panel to detect PDAC in the early stage. Two biomarker panels are suggested to recognize other stages of illness.

It can be concluded that ALB, CTNNB1, COL1A1, POSTN, LUM, and ANXA2 and also FN1, HSP90AA1, LOX, ANXA5, SERPINE1, and WWP2 beside GAPDH, AKT1, EGF, CASP3 are suitable sets of gene to separate stages of PDAC.

Positive role of coffee consumption on regulation of human blood sugar has been highlighted by researchers. On the other hand, metformin is the common drug against type 2 diabetes. This study aimed to explore possible ways to use coffee as a complementary agent beside metformin or independently versus type 2 diabetes. Proteomic data about effect of two major compounds of coffee (caffeine and trigonelline) on improvement of diabetic condition was searched and analyzed via protein-protein interaction (PPI) network analysis and gene ontology enrichment. Gene expression profiles of human whole blood of diabetic patients (responsive to metformin) versus control were extracted from GSE83983 which is recorded in Gene Expression Omnibus (GEO) database. After pre-evaluation of data by GEO2R program, the significant differentially expressed genes (DEGs) were assessed via PPI network analysis and regulatory network evaluation. Caffeine and trigonelline effectively regulate the glycolytic processes to fight against diabetic condition. HSP90AA1, TLR4, RELA, ARRB, LRRK2, STAT5B, LYN, and TLR2 genes that are involved in diabetes were affected significantly by metformin. It can be concluded that coffee consumption can improve sugar regulation in diabetes similar to metformin. IT seems that the optimized consumption quantity of coffee can be considered as controller of blood sugar in diabetic patients.

Sickle cell disease (SCD) is one of the hematological disorders characterized by a defect in the structure and function of globin chains. Hereditary factors play an important role in the pathogenesis of SCD. We aimed to investigate the genes and pathways related to the pathogenesis of SCD.

Microarray dataset was downloaded from the Gene Expression Omnibus (GEO) database. LIMMA package of R-software was used to detect UP and Down regulations between SCD and control subjects. En-richment analysis and Protein-protein interaction (PPI) networks were performed using GeneCodis4 software and GeneMANIA database, respectively. PrognoScan database was used to evaluate the relationship between the hub genes and patients' survival.

Overall, 447 DEGs were identified in SCD patients compared to control subjects. Out of 447 DEGs, 345 genes were up-regulated and 102 genes were down-regulated. Effective hub genes in SCD pathogenesis in-clude SLC4A1, DTL, EPB42, SNCA, andTOP2A. In addition, hub genes had a high diagnostic value.

Evaluation of hub genes in SCD can be used as a diagnostic panel to detect high-risk patients. In addition, by identifying the UP and Down stream pathways, treatment strategies in the monitoring and treat-ment of patients can be designed.

 Salmonellosis, a disease caused by Salmonella, is a significant public health concern and economic burden worldwide. The ability of various Salmonella serovars to cause disease is closely linked to the virulence genes they possess.

 The aim of this study was to develop a multiplex fluorescence PCR for detecting ten major virulence genes (ssaR, spvC, pefA, sipA, fimA, sifA, sopE2, sopB, prgH, and stn) in Salmonella.

 Primer pairs specific to ten target virulence genes were designed using Primer Premier 5.0 and distributed across two reaction tubes. The multiplex fluorescence PCR was optimized by adjusting one factor at a time.

 A total of sixty Salmonella strains were analyzed using the newly developed multiplex fluorescence PCR. All strains contained seven or more of the tested virulence genes. The positive rates of virulence genes ssaR, sipA, sopE2, sopB, prgH, and stn were high, each at 100%. The positive rate of sifA was also relatively high at 81.67%. However, the positive rates of spvC at 5% and pefA at 3.33% were relatively low.

 The newly developed multiplex fluorescence PCR provides a straightforward, cost-effective, and high-throughput solution for detecting virulence genes in Salmonella. It has the potential to become a routine method for analyzing Salmonella virulence genes.

Amphotericin B is a broad-spectrum antifungal agent commonly used to treat Candida haemulonii infection. C. haemulonii was isolated from patients reported to be intrinsically resistant to amphotericin B, encoded by the ERG2 and ERG11 genes. However, there have been limited studies concerning amphotericin B-resistant C. haemulonii in Indonesia. The objective of this study is to explore the phenotypic and genotypic characteristics (ERG2 and ERG11) of C. haemulonii isolated from the ICU of a referral hospital in Indonesia.

Identification and susceptibility tests were conducted using VITEK2. Thereafter, DNA was extracted and amplified using conventional PCR followed by DNA sequencing (Sanger method).

The results of the phenotypic susceptibility test showed that all C. haemulonii were resistant to amphotericin B. ERG2 and ERG11 sequences showed the same amino acid sequence and corresponded to references that are resistant to amphotericin B.

The resistant properties of C. haemulonii against amphotericin B found in this study require further exploration, including comparing resistant and sensitive C. haemulonii to amphotericin B. In addition, it is necessary to analyze other genes besides ERG2 and ERG11.

This study explores the association between growth arrest-specific 5 (GAS5) rs145204276, nuclear paraspeckle assembly transcript 1 (NEAT1) rs512715, and Maternally Expressed 3 (MEG3) rs4081134 polymorphisms and their impact on susceptibility to papillary thyroid carcinoma (PTC), considering differential expression of long noncoding RNAs (lncRNAs) in PTC.

A case-control study involving 125 papillary thyroid carcinoma (PTC) patients and 125 controls was conducted. Genotyping of polymorphisms was performed using tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP) methods.

No significant association was found between the two groups regarding genotypes and allelic frequencies of GAS-5 145204276 and MEG3 rs4081134 polymorphisms. Genetic models also showed the same results. Regarding NEAT1 rs512715, The PTC group had more GC genotypes and over-dominant models of NEAT1 rs512715 than controls, while controls showed a higher frequency of recessive models.

GAS5 rs145204276 and MEG3 rs4081134 polymorphisms showed no significant association with papillary thyroid carcinoma (PTC) risk. In contrast, NEAT1 rs512715 exhibited a significant impact on PTC development.

Breast cancer is one of the most common malignancies in women for which no suitable treatment has been found yet. Therefore, the present study studied the cytotoxicity effects of tyrosol (TRY) on the Michigan Cancer Foundation-7 (MCF7) breast cancer cell line and L929 normal cells.

MCF7 and L929 cells were cultured red in DMEM-F12 culture medium after preparation and then exposed to 0, 100, 200, and 300 μM of TRY for 72 hours. Cell viability was evaluated using the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay, and apoptotic and necrotic cell percentages were determined by flow cytometry. After designing specific primers, the expression levels of bax, p53, and bcl-2 genes were evaluated by RT-PCR. GraphPad Prism software was used for analyzing the data.

TRY-treated MCF7 cells showed significantly decreased cell viability in a dose-depended manner. Also, the cell treated with high concentrations of TRY (200 and 300 µM) had a high rate of apoptosis and necrosis (P<0.0001). Reactive oxygen species (ROS) content increased in TRY-treated MCF7 cells. Moreover, the overexpression of bax and p53 and downregulation of bcl-2 was seen in TRY-treated MCF7 cells.

TRY has anticancer effects on breast cancer cells by the induction of oxidative stress and apoptosis, as well as the regulation of genes involved in the process of mitochondrial apoptosis.

Breast cancer is one of the common malignancies in women, for which doxorubicin (DOX) is widely used in its chemotherapy. Recently, it has been found that DOX affects the expression profile of oncogene genes and miRNAs. In this study, the impacts of DOX on the expressions of the STAT3 gene, miR-874-3p, and miR-337-3p were studied in the MCF-7 breast cancer cell line.

After exposure of MCF-7 cells with DOX, the MTT method was applied for evaluating the cell viability. Apoptosis and necrosis percentages were measured using flow cytometry. Also, the levels of ROS and NF-κB were measured in DOX-treated cells. Then, exosomes secreted from these cells were prepared. The shape of exosomes was studied by SEM. Finally, the expression of bax, bcl-2, p53, casp3, STAT3 gene, and miR-874-3p and miR-337-3p in MCF-7 cells as well as exosomes were evaluated using the RT-PCR technique. Data analysis was done by T-test in GraphPad Prism8 software.

The exposure of MCF-7 cells to doxorubicin led to a concentration-dependent decrease in cell viability and increases in apoptosis and necrosis. ROS and NF-κB activity were increased in DOX-treated cells. In DOX-treated cells, decreased expressions of bcl-2 and STAT3 genes and overexpression of bax, p53, casp3, miR-874-3p, and miR-337-3p were observed compared to untreated control cells.

One of the mechanisms of the anti-breast cancer effects of DOX is the induction of changes in the expression of oncogenic genes, mediating by downregulating of STAT3 gene and overexpressing miR-874-3p and miR-337-3p. More studies are needed in this field.

Gastric cancer is an invasive cancer, which is usually diagnosed in advanced stages. However, the markers affecting its progression, and invasion are of great importance in its diagnosis and treatment. The current research aimed to study the correlation of genes that contributed to epithelial-mesenchymal transition (EMT), Mest1, and GjA1, with some clinicopathological specifications in gastric cancer patients to better comprehend the functions of these genes in this tumor.

RNA was extracted from the tumor, and normal tissues and cDNA were synthesized. Then, by designing specific primers for Gja1 and Mest1 genes, their expressions were studied by RT-PCR. The data was analyzed by GraphPad Prism 8 software.

Significant differences among the expressions of the mentioned genes associated with clinicopathological variables of gastric cancer patients, including tumor size, grade, stage, metastasis, and lymphatic invasion were seen.

The obtained data showed the important role of EMT-related genes, Gja1 and Mest1 in the clinical progression of the tumor. Further studies with larger sample sizes are required to confirm these genes as biomarker candidates for detecting gastric cancer.

Wound healing is a complex process involving the coordinated interaction of various genes and molecularpathways. The study aimed to uncover novel therapeutic targets, biomarkers and candidate genes for drug developmentto improve successful wound repair interventions. This study is a network-meta analysis study. Nine wound healing microarray datasets obtainedfrom the Gene Expression Omnibus (GEO) database were used for this study. Differentially expressed genes (DEGs)were described using the Limma package and shared genes were used as input for weighted gene co-expressionnetwork analysis. The Gene Ontology analysis was performed using the EnrichR web server, and construction of aprotein-protein interaction (PPI) network was achieved by the STRING and Cytoscape. A total of 424 DEGs were determined. A co-expression network was constructed using 7692 shared genesbetween nine data sets, resulting in the identification of seven modules. Among these modules, those with the top 20genes of up and down-regulation were selected. The top down-regulated genes, including TJP1, SEC61A1, PLEK,ATP5B, PDIA6, PIK3R1, SRGN, SDC2, and RBBP7, and the top up-regulated genes including RPS27A, EEF1A1,HNRNPA1, CTNNB1, POLR2A, CFL1, CSNk1E, HSPD1, FN1, and AURKB, which can potentially serve as therapeutictargets were identified. The KEGG pathway analysis found that the majority of the genes are enriched in the "Wntsignaling pathway". In our study of nine wound healing microarray datasets, we identified DEGs and co-expressed modulesusing WGCNA. These genes are involved in important cellular processes such as transcription, translation, and posttranslationalmodifications. We found nine down-regulated genes and ten up-regulated genes, which could serve aspotential therapeutic targets for further experimental validation. Targeting pathways related to protein synthesis and celladhesion and migration may enhance wound healing, but additional experimental validation is needed to confirm theeffectiveness and safety of targeted interventions.

Primary ciliary dyskinesia (PCD) is considered a monogenic heterogeneous recessive disorder.

This study aimed to identify clinical characteristics and gene mutations in children with PCD admitted to Quanzhou Women’s and Children’s hospital in China from January 2019 to January 2022.

Clinical manifestations, lung imaging, transmission electron microscopy (TEM) findings, and genetic test results were analyzed in this study.

For 8 patients, PCD manifestations included asthma, total visceral inversion, secretory otitis media, adenoid hypertrophy, gastroesophageal reflux, intestinal malrotation withmidguttorsion, andbronchiectasis. Primary ciliary dyskinesia-associated gene variants included DNAH11, DNAH5, RSPH4A, and CFAP300. Novel variants of DNAH11 (c.5460 + 5G > C, c.117499_11752delGTTA, and c.5822G > C), DNAH5 (c.4314delT and c.877dupA), RSPH4A (c.1774_1775delTT and c.1949A > G), and CFAP300 (c.603delG) were found in these children.

Recurrent cough, expectoration, purulent discharge, bronchiectasis, and visceral inversion provide clues for diagnosing early-onset PCD. Transmission electron microscopy and genetic testing improve early diagnosis, treatment delivery, and prognosis. Novel genotypes identified in this study expand the PCD genotypic spectrum.

 Investigations indicate that Wedelia chinensis extract increases efficacy of prostate cancer treatment. In the present study, the differentially expressed genes (DEGs) of prostate cancer cell line 22RV1 in the presence of W. chinensis extract derived from Gene Expression Omnibus (GEO) were evaluated by gene ontology and pathway analysis. 

 Gene expression profiles of GSE100224 were analyzed by GEO2R. The significant DEGs were assessed via action map analysis. The related biological terms were identified for the significant DEGS. The highlighted dysregulated genes and pathways were discussed. 

 Seventy significant DEGs including 49 up-regulated genes and 21 down-regulated ones were assessed by inhibition, activation, expression, and binding actions. Cytochrome P450 and PTGS2 were highlighted as the crucial DEGs. Estrogen metabolism was pointed as the main targeted pathway.  

 Findings indicated that “estrogen metabolism” and UGT1A1, MAOA, PTSG2, and cytochrome P450 in the 22RV1 cells were the main targeted pathway and genes by W. chinensis .

Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus pyogenes are among the most important causes of infection in human. Inventing rapid methods to identify these species can help in providing appropriate and effective treatment options. Therefore, the current study aimed to develop a multiplex touch-down PCR method to identify rapidly the aforementioned species patients' sputum samples, simultaneously.

A total of 50 sputum samples of patients with respiratory infections resistant to treatment were collected. After DNA extraction and primer design, the complete capsule (CAP) region II, capsular polysaccharide biosynthesis (cpsA) and the structural regulator of transcription (spy) genes were amplified for detecting H. influenzae, S. pneumoniae and S. pyogenes by multiplex touch-down PCR.

Among 50 samples prepared from patients with different diseases, 27 samples were positive for amplified genes. The frequency of presence of pathogens in the collected samples included 14% H. influenzae, 20% S. pneumoniae and 20% S. pyogenes. Also, in some patients, the simultaneous presence of two or three pathogens were observed.

In general, it can be concluded that the PCR touchdown method developed in the present study is an effective and fast method for the simultaneous identification of H. influenzae, S. pneumoniae and S. pyogenes pathogens in clinical samples of patients.

Ex vivo blood production is an urgent need of most countries, and creating production protocols can save the lives of many patients. Despite the recent advances in blood production in ex vivo conditions, its high-scale production is not yet possible, and requires further studies. Therefore, by transfecting fibroblast cells with miR-16, and miR-451 genes, as well as applying low frequency electromagnetic fields (ELF-EMF) treatment, we tried to increase the differentiation of these cells into CD71+ and CD235a+ erythroid like progenitors.

After preparation, and cultivation of human dermal transgenic fibroblast cells, they were transfected by Plenti3-hsa-miR451, Plenti3-hsa-miR16 and Plenti3-backbone inserted into E. coli Stbl4 genome. Then, transgenic fibroblast cells were treated with 10mT ELF-EMF every day for 20 minutes for 7 days. Using a flow cytometer, the expressions of CD71, and CD235a were studied in these cells, and the expressions of genes involved in hematopoiesis were studied using the RT-PCR technique.

The results indicated an increase in the differentiation of fibroblast cells treated with 10mT ELF-EMF to erythroid like progenitors. Furthermore, the percentage of CD71+ and CD235a+ cells was the highest in irradiated cells encoding miR-16 and miR-451, which indicates their differentiation into erythroid like progenitors. Also, in the transgenic cells treated with ELF-EMF, an increase in the expressions of α-chain, β-chain, γ-chain and GATA1 genes was observed, which indicates the potential of these cells for hematopoiesis. However, there was no significant difference in the expression of CD34 and CD38 genes in these cell lines.

Both ELF-EMF and upregulations of miR-16 and miR-451 lead to improved differentiation of fibroblast cells into erythroid like progenitors.

More than 80 genes are involved in the pathogenesis of the most common single gene peripheral neuropathies denoted as Charcot-Marie-Tooth (CMT). Only a few studies have investigated the pathological molecular mechanisms of Iranian patients affected with CMT. The aim of this study is to identify the clinical manifestation, mutational spectrum and phenotypic correlation of a cohort of patients with Charcot-Marie-Tooth disease (CMT) in Iran.

We conducted a comprehensive gene panel sequencing consisting of 80 genes in a cohort of 23 patients with CMT referred between January 2015 and March 2021. The recruited samples indicated almost an equal distribution of demyelinating and axonal types of CMT, with practically no difference between AD or AR patterns of inheritance.

Four novel mutations, including c.271C>T in LITAF and c.205+1delG in NDRG1, c.2455A>C in KIF1B and c.1728A>G in FIGF were detected in four patients affected with demyelinating CMT types (CMT1C and CMT4D), and characterized phenotypically.

Our promising results unravel the complicated genetic architecture of Iranian CMT patients and help physicians and researchers achieve earlier diagnosis, better clinical management and recognizing high risk families. Further large-scale studies are needed to improve our understanding of CMT complex genetic architecture

Photodynamic therapy (PDT) is a method based on the application of a photosensitive agent and the administration of light irradiation on the treated samples. PDT is applied as an effective tool with minimal side effects against tumor tissues. This study aimed to assess the targets of critical genes by PDT at the cellular level of cancer to provide a new perspective on its molecular mechanism.

To assess the effect of PDT, we extracted the differentially expressed genes (DEGs) from the gene expression profiles of human umbilical vein endothelial cells (HUVECs) treated with PDT from Gene Expression Omnibus (GEO) databases. The queried DEGs were evaluated via a regulatory network and gene ontology enrichment to find the critical targets.

Among 76 queried significant DEGs, 27 individuals were interacted by activation, inhibition, and co-expression actions. Thirty DEGs were related to the five classes of biological terms. The IL-17 signaling pathway and PTGS2, CXCL8, FOS, JUN, CXCL1, ZFP36, and FOSB were identified as the crucial targets of PDT.

PDT as a stimulator of gene expression and an activator of gene activity overexpressed and hyper-activated many genes. It seems that PDT introduces a number of genes and pathways that can be regulated by anticancer drugs to fight against cancers.

Extracorporeal photopheresis (ECP) is a therapeutic method applied against some diseases such as cancers. Using 8-methoxypsoralen (8-MOP) and UVA radiation in ECP is associated with achievement in the treatment of patients with leukemic cutaneous T-cell lymphoma (CTCL). Evaluation of cellular resistance versus ECP is the aim of this study.

Data were downloaded from the Gene Expression Omnibus (GEO) database and were analyzed via the GEO2R program. The significant DEGs were assessed via protein-protein interaction (PPI) network analysis by using the STRING database and Cytoscape software. The critical genes were evaluated via gene ontology by using the ClueGO application of Cytoscape software. The identified biological processes were determined and analyzed.

Fifty-seven significant DEGs were determined. The main connected component of the PPI network including 32 queried significant DEGs plus 50 first neighbors was constructed. Nineteen histones as critical nodes were assessed via gene ontology, and “nucleosome organization” was pointed out as the crucial biological process. Finally, 15 histones from H2A, H2B, and H3 histone families were identified as the key genes that are involved in the resistance property of the treated cells.

In conclusion, 15 members of H2A, H2B, and H3 families (especially H2A family) were considered as the origin of resistance versus ECP treatment. It is concluded that sensitivity to ECP treatment depends on gross molecular events which are involved in the functions of histones.