Long non-coding RNAs as potential biomarkers or therapeutic targets in gastric cancer.

Aim: This study aimed to find lncRNAs and mRNAs that were expressed differently by combining microarray datasets from different studies. This was done to find important target genes in gastric cancer for anti-cancer therapy. Background: Gastric cancer (GC) is the fourth most frequent and second-most deadly malignancy worldwide. Thus, genetic diagnosis and treatment should focus on genetic and epigenetic variables. Based on several studies, disordered expression of non-coding RNAs (ncRNAs), such as lncRNAs, regulate gastric cancer invasion and metastasis. Besides, lncRNAs cooperatively regulate gene expression and GC progression. Methods: We obtained differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) from three GC tissue microarray datasets by meta-analysis and screened genes using the "Limma" package. Then, using the RNAInter database, we allocated DEmRNAs to each DElncRNA. ClusterProfiler and GOplot programs were used to analyze function enrichment pathways and gene ontologies for final DEmRNAs. Results: A total of 9 differentially expressed lncRNAs (DElncRNAs) (5 up-regulated and 4 down-regulated), and 856 DEmRNAs (451 up-regulated and 405 down-regulated) between tumor and adjacent normal samples were found. Finally, 117 differentially expressed mRNAs were predicted as interactors of six DElncRNAs (H19, WT1-AS, EMX2OS, HOTAIR, ZEB1-AS1, and LINC00261). Conclusion: In order to promote cancer therapeutics and give knowledge on the process of carcinogenesis, our study projected a network of drug-gene interactions for discovered genes and presented relevant prospective biomarkers for the prognosis of patients with stomach cancer.

Anti-aging effects of the pistachio extract on mesenchymal stem cells proliferation and telomerase activity.

PURPOSE: Using mesenchymal stem cells (MSCs) is a promising method in regenerative medicine. Limited proliferation and aging process of MSC are the most common problems in MSCs application. In the present study, we intend to investigate the anti-aging properties of pistachio pericarp in bone marrow-derived MSCs of old male rats. MATERIALS AND METHODS: First, 1000, 2000, and 3000 µg/mL AEPP were used to treat MSCs derived from bone marrow for 24 h at 37 °C. Then, cell viability, population doubling time, the percentage of senescent cells, telomere length, telomerase activity, and the expression of TRF1 and RAP1 when bone marrow-derived MSCs treated with AEPP were investigated. RESULTS: The results showed that cell viability increased when MSCs derived from bone marrow were treated with 2000 and 3000 µg/mL AEPP, indicating this extract may stimulate proliferation. The population doubling time was also enhanced with an increase in AEPP concentration. Importantly, an increase in AEPP concentration significantly reduced senescent cell percentage. Telomere length, telomerase activity, and the expression of anti-aging genes were significantly increased with the increase of AEPP dose. CONCLUSION: Taken together, AEPP has been used as a natural compound with excellent proliferation and anti-aging ability in MSCs. As new therapeutic candidates with promising effects, it can be used with high safety by multiplying cells and delaying the aging process. However, more studies are needed and the anti-aging effects of this extract should be well confirmed in animal models and clinical trials.

In vitro and Pharmacoinformatics-based phytochemical screening for anticancer impacts of pistachio hull essential oil on AGS, PLC/PRF/5, and CACO2 cell lines.

BACKGROUND: The essential oil of pistacia vera (cv. Ohadi) hull (PHEO) was checked using gas chromatography mass spectrometry (GC/MS) analysis. It was studied the genes of the wnt pathway with a certain concentration of PHEO on Human gastric cancer (AGS), human hepatocellular carcinoma (PLC/PRF/5), and human colon cancer (CACO2) cell lines. METHODS AND RESULTS: After evaluating the survival rate of cancer cells by MTT test and determining IC50, pistachio hull essential oil (PHEO) was used for 24-hours to treat the cells. After RNA extraction, the expression of wnt pathway genes was evaluated by Real-Time PCR. Considering the crucial role of ß-catenin accumulation and its effect on the progression of gastrointestinal cancers, Western blot analysis was also used to determine the effect of PHEO in protein expression of ß-catenin inhibition. Also, an in silico analysis was carried out to investigate the effect of PHEO extracted compounds on protein expression of ß-catenin and FZD7 inhibition. According to the results, wnt pathway genes were changed in samples treated using PHEO. The results showed the up-regulation of GSK-3ß and down-regulation of Wnt-1, LEF-1, TCF1, and CTNNB1 genes compared to the control. CONCLUSION: We showed inhibition of ß-catenin protein in cancer cell lines. Four compounds of PHEO were suggested to have an inhibition effect on ß-catenin and FZD7. These compounds can be useful in the treatment of gastrointestinal cancers. Altogether, the inhibitory role of ß-catenin protein can be very effective and can be considered one of the therapeutic goals in the treatment of gastrointestinal cancers.

Bioinformatics-based identification of miRNAs, mRNA, and regulatory signaling pathways involved in esophageal squamous cell carcinoma.

Aim: The current study analyzed the miRNA microarray dataset (GSE66274) and gene expression microarray dataset (GSE38129) with similar samples to achieve a better understanding of miRNA-mRNA interactions. Background: The most common form of esophageal cancer is esophageal squamous cell carcinoma (ESCC). While, miRNAs are well recognized as having a critical regulatory role in human cancer, their responsibilities and mechanisms of miRNA-mRNA in ESCC are unknown. Methods: Differentially expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) were identified using the LIMMA package in R. In total, 478 DEmRNA (224 upregulated and 254 downregulated) and 39 DEmiRNA (15 upregulated and 24 downregulated) were screened. The RNAInter database analyzed miRNA-mRNA interactions; then, the miRNA-mRNA network was visualized by Cytoscape software. ClusterProfiler packages were used to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEmRNA as targets of DEmiRNAs. Results: KEGG pathway analysis indicated that the p53 signaling pathway, ECM-receptor interaction, and AGE-RAGE signaling pathway were significant. Cellular response to amino acid stimulus, negative regulation of apoptotic signaling pathway, and endoderm formation were most prevalent in the biological process category. Additionally, the collagen-containing extracellular matrix, actomyosin complex collagen trimers, basement membrane, and extracellular matrix structural constituent were more enriched. Conclusion: Overall, the present survey provides evidence that could support the prognosis of esophageal tumors in the future.

The effect of iron sulfate nanoparticles and their fortified bread on Wistar rats and human cell lines.

BACKGROUND: Ferrous sulfate nanoparticles (FSNPs) were synthesized and characterized to mitigate the undesirable effects of ferrous sulfate bulk particles (FSBPs) as a supplement or fortificant in health/food industries. METHODS: The toxicity of FSNPs and FSBPs was evaluated against AGS, PLC/PRF/5, and HGF1-PI 1 cell lines. Then, Wistar rats were fed three levels of FSNPs and FSBPs fortified-bread. Growth performance, hematological parameters, and histopathological changes in treated rats were assessed after 21 days. RESULTS: High concentrations of FSNPs (3.125 and 6.25 mM) increased the necrosis of AGS cells. A low level of FSNPs (1.57 mM) did not affect the viability of cells after 72 h. Fibroblasts did not show apoptosis and necrosis after exposing 1.57 mM of FSNPs. In rats, 9 mg elemental iron of FSNPs/day enhanced hemoglobin, PCV, and ferritin values and increased the body weight gain (p < 0.05). FSNPs fortified-bread induced no clinical symptom or histopathological lesion in rats. CONCLUSION: FSNPs affect cells in a dose-dependent manner. The results indicate that FSNPs at the low level do not have adverse effects on normal fibroblasts and rats. Significant weight gain in rats having a low level of FSNPs compared to the FSBPs indicates the negligible toxicity of FSNPs at low concentrations.

Investigation of genes and pathways involved in breast cancer subtypes through gene expression meta-analysis.

BACKGROUND: Molecular-based studies have revealed heterogeneity in Breast cancer BC while also improving classification and treatment. However, efforts are underway to distinguish between distinct subtypes of breast cancer. In this study, the results of several microarray studies were combined to identify genes and pathways specific to each BC subtype. METHODS: Meta-analysis of multiple gene expression profile datasets was screened to find differentially expressed genes (DEGs) across subtypes of BC and normal breast tissue samples. Protein-protein interaction network and gene set enrichment analysis were used to identify critical genes and pathways associated with BC subtypes. The differentially expressed genes from meta-analysis was validated using an independent comprehensive breast cancer RNA-sequencing dataset obtained from the Cancer Genome Atlas (TCGA). RESULTS: We identified 110 DEGs (13 DEGs in all and 97 DEGs in each subtype) across subtypes of BC. All subtypes had a small set of shared DEGs enriched in the Chemokine receptor bind chemokine pathway. Luminal A specific were enriched in the translational elongation process in mitochondria, and the enhanced process in luminal B subtypes was interferon-alpha/beta signaling. Cell cycle and mitotic DEGs were enriched in the basal-like group. All subtype-specific DEG genes (100%) were successfully validated for Luminal A, Luminal B, ERBB2, and Normal-like. However, the validation percentage for Basal-like group was 77.8%. CONCLUSION: Integrating researches such as a meta-analysis of gene expression might be more effective in uncovering subtype-specific DEGs and pathways than a single-study analysis. It would be more beneficial to increase the number of studies that use matched BC subtypes along with GEO profiling approaches to reach a better result regarding DEGs and reduce probable biases. However, achieving 77.8% overlap in basal-specific genes and complete concordance in specific genes related to other subtypes can implicate the strength of our analysis for discovering the subtype-specific genes.

A new insight into sex-specific non-coding RNAs and networks in response to SARS-CoV-2.

SARS-CoV-2 is the RNA virus responsible for COVID-19, the prognosis of which has been found to be slightly worse in men. The present study aimed to analyze the expression of different mRNAs and their regulatory molecules (miRNAs and lncRNAs) to consider the potential existence of sex-specific expression patterns and COVID-19 susceptibility using bioinformatics analysis. The binding sites of all human mature miRNA sequences on the SARS-CoV-2 genome nucleotide sequence were predicted by the miRanda tool. Sequencing data was excavated using the Galaxy web server from GSE157103, and the output of feature counts was analyzed using DEseq2 packages to obtain differentially expressed genes (DEGs). Gene set enrichment analysis (GSEA) and DEG annotation analyses were performed using the ToppGene and Metascape tools. Using the RNA Interactome Database, we predicted interactions between differentially expressed lncRNAs and differentially expressed mRNAs. Finally, their networks were constructed with top miRNAs. We identified 11 miRNAs with three to five binding sites on the SARS-COVID-2 genome reference. MiR-29c-3p, miR-21-3p, and miR-6838-5p occupied four binding sites, and miR-29a-3p had five binding sites on the SARS-CoV-2 genome. Moreover, miR-29a-3p, and miR-29c-3p were the top miRNAs targeting DEGs. The expression levels of miRNAs (125, 181b, 130a, 29a, b, c, 212, 181a, 133a) changed in males with COVID-19, in whom they regulated ACE2 expression and affected the immune response by affecting phagosomes, complement activation, and cell-matrix adhesion. Our results indicated that XIST lncRNA was up-regulated, and TTTY14, TTTY10, and ZFY-AS1 lncRN as were down-regulated in both ICU and non-ICU men with COVID-19. Dysregulation of noncoding-RNAs has critical effects on the pathophysiology of men with COVID-19, which is why they may be used as biomarkers and therapeutic agents. Overall, our results indicated that the miR-29 family target regulation patterns and might become promising biomarkers for severity and survival outcome in men with COVID-19.

The immune response against Toxoplasma gondii in BALB/c mice induced by mannose-modified nanoliposome of excreted/secreted antigens.

This study aimed to compare the immune response against Toxoplasma gondii (T. gondii) in BALB/c mice induced by excreted/secreted (E/S) antigens and mannose-modified nanoliposome of E/S antigens. Here, E/S antigens and mannose-modified nanoliposome of E/S antigens were firstly prepared, and then BALB/c female inbred mice were separately immunized. In the next step, anti-E/S antigen antibodies and the relative expression levels of IL-10 and IL-12 mRNA were detected by ELISA and real-time PCR, respectively. After immunization, mice were intraperitoneally challenged with 102 tachyzoites of T. gondii, and the survival rate was recorded. The ELISA analysis showed significant differences between the levels of anti-E/S antigen antibodies in the mice immunized by E/S antigens and those immunized by mannose-modified nanoliposome of E/S antigens at days 7, 10, 20, 25, and 30 (P < 0.05). Real-time PCR analysis showed that the relative expression of IL-10 was significantly decreased during 20 days. Yet, the relative expression of IL-12 was significantly increased during 20 days (P < 0.05). In T. gondii challenge test, significant differences were found between the survival rates of mice immunized by E/S antigens and mice immunized by mannose-modified nanoliposome with E/S antigens. This project evidenced that mannose-modified nanoliposome of E/S antigens induced a more powerful immune response against T. gondii in BALB/c mice when compared with excreted/secreted antigens alone.

Electrochemical determination of rutin by using NiFe2O4 nanoparticles-loaded reduced graphene oxide.

A binary transition metal oxide containing nickel and iron (NiFe2O4) and hybridization of this nanomaterial with reduced graphene oxide (rGO) are synthesized by the hydrothermal method. X-ray diffraction (XRD) and Raman spectroscopy confirm the successful synthesis of these materials. Also, scanning electron microscope (SEM) and transmission electron microscope (TEM) images illustrated the particle morphology with the particle size of 20 nm. The synthesized material is then examined as a sensor on the surface of the glassy carbon electrode to detect a very small amount of rutin. Some electrochemical tests such as cyclic voltammetry, differential pulse voltammetry (DPV), and impedance spectroscopy indicate the remarkable accuracy of this sensor and its operation in a relatively wide range of concentrations of rutin (100 nM-100 µM). The accuracy of the proposed electrochemical sensors is approximately 100 nM in 0.1 M PBS, (pH = 3) which is relatively impressive and can be reported. Also, the stability rate after 100 DPV was about 95 %, which is a considerable and relatively excellent value. Considering the very good results, it seems that the NiFe2O4-rGO can be considered as a new proposal in the development of accurate and inexpensive electrochemical sensors.

Design, synthesis and biological assessment of acridine derivatives containing 1,3,4-thiadiazole moiety as novel selective acetylcholinesterase inhibitors.

A novel series of acridine derivatives containing substituted thiadiazol-2-amine moiety was synthesized via multi-component condensation reaction of dimedone, aromatic aldehyde and 5-aryl-1,3,4-thiadiazol-2-amines in the presence of LaCl3 as a catalyst under solvent-free conditions. Anticholinesterase (AChE and BuChE) activity evaluation of the derivatives showed that all the derivatives are capable of inhibiting both enzymes and are highly selective towards AChE. Among them, the ability of 4i and 4d with respective IC50 values of 0.002 and 0.006 µM to inhibit AChE was higher than the reference compound tacrine (IC50 = 0.016 µM). The kinetics studies demonstrated that 4i and 4d inhibit AChE through a competitive/non-competitive mixed mechanism. The HEPG2 cell viability assay evidenced that 4i and 4d significantly exhibit lower hepatotoxicity compared with tacrine. Blind docking experiments performed on TcAChE (PDB ID: 2ACE) indicated that an unknown site is preferred for binding by all the derivatives over classic binding site of the enzyme, site 1 (CAS/PAS). Identification of the residues by protein structure alignment confirmed that this site is site 2 which was recently recognized as a new allosteric site of hAChE. The binding modes of 4i and 4d were also investigated using local docking studies on site 1 and site 2.

The Blepharis persica seed hydroalcoholic extract synergistically enhances the apoptotic effect of doxorubicin in human colon cancer and gastric cancer cells.

The goal of this survey is to evaluate the anti-proliferative effects of the hydroalcholic extract of Blepharis persica seeds and its synergic effect on doxorubicin (DOX) in human colon cancer (HT-29) and gastric cancer cell (AGS) lines. 70% Ethanol was used for extraction of B. persica seed. Aluminum-chloride colorimetric and Folin-Ciocalteu reagent methods were used to measure total flavonoid and total phenolic contents of the extract respectively. Gas chromatography-mass spectrometry (GC-MS) analysis of the B. persica extract was performed on GC-MS equipment after silylation. HT-29, AGS, and human fibroblast (SKM) cell lines were treated by different concentration of the B. persica extract, (DOX) and the combination of extraction and DOX. The cytotoxicity was measured using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay while the apoptosis induction was monitored using flowcytometry by annexin-V FITC/PI double-staining. The changes in expression levels of BAX and BCL-2 were determined using Real-Time RT-qPCR. GC-MS analysis of the hydroalcoholic extract from B. persica seeds revealed 24 major components. The MTT assay revealed the cytotoxicity against three cell lines and also it was shown that 125 ng/mL of DOX and 0.625 mg/mL of B. persica extract had synergistic behavior against HT29 cell line. These results showed B. persica extract induced apoptosis in AGS and HT29 cells and its extract caused dose-dependent increase in up-regulation of BAX level (p < 0.05) and down-regulation of BCL2 (p < 0.05). B. persica showed the synergistic effect in combination with DOX on HT29 cell line. These findings demonstrated a basis for further studies on the characterization and mechanistic evaluation of the bioactive compounds of B. persica extract which had antiproliferative effects on cancer cell lines.

Genetic analysis of an F2 intercross between two strains of Japanese quail provided evidence for quantitative trait loci affecting carcass composition and internal organs.

The purpose of this study was to identify genomic regions, quantitative trait loci (QTL), affecting carcass traits on chromosome 1 in an F2 population of Japanese quail. For this purpose, two white and wild strains of Japanese quail (16 birds) were crossed reciprocally and F1 generation (34 birds) was created. The F2 generation was produced by intercrossing of the F1 birds. Phenotypic data including carcass weight, internal organs and carcass parts were collected on F2 animals (422 birds). The total mapping population (472 birds) was genotyped for 8 microsatellite markers on chromosome 1. QTL analysis was performed with interval mapping method applying the line-cross model. Significant QTL were identified for breast weight at 0 (P < 0.01), 172 (P < 0.05) and 206 (P < 0.01), carcass weight at 91 (P < 0.05), carcass fatness at 0 (P < 0.01), pre-stomach weight at 206 (P < 0.01) and uropygial weight gland at 197 (P < 0.01) cM on chromosome 1. There was also evidence for imprinted QTL affecting breast weight (P < 0.01) on chromosome 1. The proportion of the F2 phenotypic variation explained by the significant additive, dominance and imprinted QTL effects ranged from 1.0 to 7.3%, 1.2 to 3.3% and 1.4 to 2.2%, respectively.

Human Dental Pulp Stem Cells Differentiate into Oligodendrocyte Progenitors Using the Expression of Olig2 Transcription Factor.

The helix-loop-helix transcription factor Olig2 is essential for lineage determination of oligodendrocytes. Differentiation of stem cells into oligodendrocytes and transplanting them is a novel strategy for the repair of different demyelination diseases. Dental pulp stem cells (DPSCs) are of great interest in regenerative medicine due to their potential for repairing damaged tissues. In this study, DPSCs were isolated from human third molars and transfected with the human Olig2 gene as a differentiation inducer for the oligodendrogenic pathway. Following the differentiation procedure, the expression of Sox2, NG2, PDGFRα, Nestin, MBP, Olig2, Oct4, glial fibrillary acidic protein and A2B5 as stage-specific markers was studied by real-time RT-qPCR, immunocytochemistry and Western blot analysis. The cells were transplanted into a mouse model of local sciatic damage by lysolecithin as a model for demyelination. Oligodendrocyte progenitor cells (OPCs) actively remyelinated and recovered the lysolecithin-induced damages in the sciatic nerve as revealed by treadmill exercise, the von Frey filament test and hind paw withdrawal in response to a thermal stimulus. Recovery of behavioral reflexes occurred 2-6 weeks after OPC transplantation. The results demonstrate that the expression of Olig2 in DPSCs reduces the expression of stem cell markers and induces the development of oligodendrocyte progenitors as revealed by the emergence of oligodendrocyte markers. DPSCs could be programmed into oligodendrocyte progenitors and considered as a simple and valuable source for the cell therapy of neurodegenerative diseases.