Molecular mechanism of a novel root-end filling material containing zirconium oxide on the osteogenic/odontogenic differentiation of human osteosarcoma MG-63 cells.

Although the novel root-end filling material containing zirconium oxide (NRFM-Zr) which is hydroxyapatite-based may promote osteoblast differentiation, the molecular mechanism remains unclear. The aim of this study is to investigate it underlying the osteogenic/odontogenic differentiation of human osteosarcoma MG-63 cells induced by NRFM-Zr, compared with calcium silicate-based mineral trioxide aggregate (MTA), and glass ionomer cement (GIC). Firstly, three different types of root filling materials were co-cultured with MG-63 cells, and their cell toxicity, alkaline phosphatase (ALP) activity, and calcium ion concentration were evaluated. Next, gene expression profiling microarray was employed to analyze the impact of the materials on the gene expression profile of MG-63 cells. The results of cell viability revealed that NRFM-Zr group had no significant difference compared to the negative control group. After 5 and 7 days of cultivation, both the NRFM-Zr and MTA groups exhibited significantly higher ALP activity compared to the negative control (p < 0.05). Moreover, the NRFM-Zr group had the highest calcium ion concentration, while the GIC group was the lowest (p < 0.05). Gene expression profiling microarray analysis identified 2915 (NRFM-Zr), 2254 (MTA) and 392 (GIC) differentially expressed genes, respectively. GO functional and KEGG pathway analysis revealed that differentially expressed genes of NRFM-Zr, MTA and GIC participated in 8, 6 and 0 differentiation-related pathways, respectively. Comparing the molecular mechanisms of osteogenic/odontogenic differentiation induced by hydroxyapatite-based NRFM-Zr and calcium silicate-based MTA, it was found that they shared similarities in their molecular mechanisms of promoting osteogenic differentiation. NRFM-Zr primarily promotes differentiation and inhibits cell apoptosis, thereby enhancing osteogenic/odontogenic differentiation of MG-63 cells. Furthermore, the inducing efficacy of NRFM-Zr was found to be superior to MTA.

Comprehensive gene expression analysis after ERH gene knockdown in human bladder cancer T24 cell lines.

INTRODUCTION: In this article, we utilized Ingenuity® Pathway Analysis (IPA®) bioinformatics analysis software and Metascape® bioinformatics analysis website tools to analyse the possible mechanism of ERH affecting tumourigenesis (proliferation and apoptosis) in bladder cancer (BC) T24 cells. METHODS: The ERH gene was knocked down, and BC T24 cells were divided into ERH normal and knockdown groups. Affymetrix® gene expression microarrays were performed to obtain a differentially expressed gene list (DEGL) between the 2 groups. IPA® data analyses contain five modules: disease and function analysis, upstream analysis, regulator effects analysis, canonical pathway analysis and molecular network analysis. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were analysed by Metascape®. RESULTS: The results of the gene expression profiling chip and the DEGL showed that 344 genes were upregulated and 254 genes were downregulated. The IPA® and Metascape® pathway analyses showed that the ERH gene may affect proliferation and apoptosis by affecting the apoptosis, cell cycle, Toll-like receptor (TLR), NF-κB or TGF-beta signalling pathways. Upstream analysis determined that the ERH gene may regulate TNF and NK-κB in the BC T24 cell lines. The ERH gene may be involved in the "cell death and survival" molecular network in BC T24 cells. ERH may be a regulator of KITLG through TNF. CONCLUSIONS: The ERH gene may affect apoptosis through the TLR, NF-κB, TNF or TGF-beta signalling pathways in BC T24 cells, and may be a regulator of KITLG to ultimately activate the growth of malignant tumours.

Discovery of microarray-identified genes associated with the progression of cervical intraepithelial neoplasia.

OBJECTIVE: To identify genes potentially associated with cervical intraepithelial neoplasia (CIN) progression through bioinformatic approaches and clinicopathological verification. METHODS: mRNA expression microarray data related to CIN progression were screened from the Gene Expression Omnibus (GEO) database and re-analyzed using bioinformatics approaches. Tissue microarray immunohistochemistry was conducted to assess the significant identified genes in CIN, cervical cancer, and normal tissues. RESULTS: Biological annotation and text mining showed that 14 differentially expressed genes were directly or indirectly related to CIN progression. The expression of 5 up-regulated differentially expressed genes, namely, CCND2, TGFBR2, PRKCB, SH3KBP1 and WNT2B, was examined by tissue microarray immunohistochemistry, with the known CIN progression genes P16 and Ki-67 as the internal reference. Expression of TGFBR2, SH3KBP1, and WNT2B were not detected in CIN and cervical carcinoma, whereas no significant difference in the expression rate of PRKCB was detected (P > 0.05). CCND2, P16, and Ki-67 expression showed a gradual increasing trend in normal, CIN, and cervical cancer. CONCLUSIONS: 14 differentially expressed genes were associated with CIN progression, as indicated by the microarray data analysis results. CCND2 may be a new marker for the prediction of CIN progression in addition to P16 and Ki-67.

Analysis of microarray-identified genes and microRNAs associated with drug resistance in ovarian cancer.

The aim of this study was to identify potential microRNAs and genes associated with drug resistance in ovarian cancer through web-available microarrays. The drug resistant-related microRNA microarray dataset GS54665 and mRNA dataset GSE33482, GSE28646, and GSE15372 were downloaded from the Gene Expression Omnibus database. Dysregulated microRNAs/genes were screened with GEO2R and were further identified in SKOV3 (SKOV3/DDP) and A2780 (A2780/DDP) cells by real-time quantitative PCR (qRT-PCR), and then their associations with drug resistance was analyzed by comprehensive bioinformatic analyses. Nine microRNAs (microRNA-199a-5p, microRNA-199a-3p, microRNA-199b-3p, microRNA-215, microRNA-335, microRNA-18b, microRNA-363, microRNA-645 and microRNA-141) and 38 genes were identified to be differentially expressed in drug-resistant ovarian cancer cells, with seven genes (NHSL1, EPHA3, USP51, ZSCAN4, EPHA7, SNCA and PI15) exhibited exactly the same expression trends in all three microarrays. Biological process annotation and pathway enrichment analysis of the 9 microRNAs and 38 genes identified several drug resistant-related signaling pathways, and the microRNA-mRNA interaction revealed the existence of a targeted regulatory relationship between the 9 microRNAs and most of the 38 genes. The expression of 9 microRNAs and the 7 genes by qRT-PCR in SKOV3/DDP and A2780/DDP cells indicating a consistent expression profile with the microarrays. Among those, the expression of EPHA7 and PI15 were negatively correlated with that of microRNA-141, and they were also identified as potential targets of this microRNA via microRNA-mRNA interaction. We thus concluded that microRNA-141, EPHA7, and PI15 might jointly participate in the regulation of drug resistance in ovarian cancer and serve as potential targets in targeted therapies.

Analysis of differentially expressed genes and metabolic pathways in human uveal melanoma / 中华实验眼科杂志

Background Studies showed that there exsits differential gene expression in human uveal melanoma (UM).However, the researching results are somewhat inconsistently abroad, while relevant literature is still less in China.Few domestic researches have reported the abnormalities of gene transcription level or the pathways of these genes.Objective This study was to compare the gene expression profiles between human UM and normal uvea tissues and analyze the metabolic pathways involved in these differentially expressed genes.Methods Four human UM samples were collected in Beijing Tongren Eye Center,and 4 pieces of normal uveal tissues from 4 donors served as controls.The expression of genes was detected with Human Genome U133 Plus 2.0 chip,and the expression profiles were compared between two groups.The biological functions and active pathways of the genes were analyzed by Gene Ontology Enrichment Analysis Software Toolkit (GOEAST).Results Compared with the normal controls,4 165 differential genes were screened in human UM (12.50％) ,including 1 236 up-regulated genes (3.71％) and 2 929 down-regulated genes (8.79％) ,in which the genes of raised more than 5-, 10-,50-and 100-fold were 113,21,1 and 1, respectively, and the genes of reduced by 50％ ,90％ ,98％ and 99％ were 1 053,422,33 and 5,respectively.The functions of these differentially expressed genes were associated with cellular differentiation and growth,development, cell adhension, immun response, transcriptional contol, signal transduction and anti-apoptosis.The metabolic pathways of differentially expressed genes included angiogenesis pathway, cell-cycle related protein kinase pathway and immune regulatory pathway (involving B lymphocytes and T lymphocytes).ConclusionsGene expression profiles are evidently different between human UM and normal uveal tissue.The variation of the gene profiles in human UM leads to the changes of multiple biological functions including angiogenesis and kinase pathway even immun system.It is implied that the pathogenesis of human UM is a comprehensive effect of multiple genes and biological pathways.

The gene expression profiles through activating endothelial target for acetylcholine / 中国药理学通报

Aim To investigate the effects of gene expression through activating endothelial target for acetylcholine (ETA).Methods Comparative studies were carried out to explore the distinct gene expression of carbachol and pilocarpine.Results Human coronary aortic endothelial cells were incubated with carbachol which activates ETA and muscarinic receptors and with pilocarpine which activates muscarinic receptors distinctly for 10 hours at the concentration of 100 ?mol?L -1.The endothelial gene expression was detected by BiostarH-14112S cDNA expression profiling microarrays containing 14 000 human unigenes. There were 801 differential genes totally (491 differentially expressed both by carbachol and by pilocarpine, 310 differentially expressed by carbachol exclusively). We found a significant increase in expression of 119 and a significant decrease in expression of 191 genes after treatment by carbachol preferentially. And these genes were not affected by pilocarpine. Further globally functional catagorization indicates that there are seven types of distinct expressed genes induced by carbachol selectively including membrane receptors and G proteins, ion channels, G protein coupled receptors, transcriptional factors, apoptosis-related genes, cell adhesive factors, thrombosis and atherosclerosis-related genes.Conclusion The differentially expressed genes evoked by carbachol exclusively are closely associated with ETA and its effectors.