This study was purposed to characterize the effect of carboxylic acid metabolite (SR26334) of clopidogrel bisulfate deprived of antiplatelet efficacy on the spectrum of gene expression in the cultured human umbilical vein endothelial cell (HUVEC) line (EA.hy926), and to explore the potential molecule mechanism of SR26334 impact on HUVEC. By using a Affymetrix HU133 plus 2.0 oligonucleotide microarray, the alteration of gene expression spectrum induced by SR26334 in HUVEC was detected, the real-time PCR was used to confirm the results of selected differentially expressing genes. The results indicated that total 235 including 176 up-regulated and 59 down-regulated genes were obtained with change more than 1.5-fold after SR26334 (10 µmol/L) acted on HUVEC for 48 h. SR26334 affected the expression levels of genes involved regulation of transcription, transcription, positive regulation of transcription from RNA polymerase II promoter, cell cycle, cell division, protein amino acid dephosphorylation in HUVEC. It is concluded that carboxylic acid metabolite SR26334 of clopidogrel bisulfate modulates function of endothelial cells through different pathway at gene level.
Cell Line ; Human Umbilical Vein Endothelial Cells ; cytology ; drug effects ; Humans ; Ticlopidine ; analogs & derivatives ; pharmacology ; Transcriptome ; drug effects

OBJECTIVE: To investigate the molecular mechanism of trichloroethylene (TCE) cardiac developmental toxicity on zebrafish embryos and to try to provide experimental data for related intervention. METHODS: Zebrafish embryos were purchased from the National Zebrafish Resource Center. The embryos were divided into DMSO(control group), DMSO+CHIR, DMSO+XAV, TCE, TCE+CHIR and TCE+XAV groups(TCE at the concentration of 1, 10 and 100 ppb, with the DMSO as control; DMSO: Dimethyl suldoxide; CHIR: CHIR-99021, Wnt agonist; XAV: XAV-939, Wnt antagonist), 60 embryos per group. Zebrafish embryos were fed in systematic aquaculture water, 28℃. The water was replaced every 24 h and drugs were added according to the grouping scheme. The cardiac tissues were dissected and analyzed by transcriptome microarray after RNA extraction. The expressions of Wnt signaling pathway related genes were verified by q-PCR. Wnt atagonist XAV and activator CHIR were used alone or in combination to further evaluate the possibility of the Wnt signaling participating in the cardiac developmental toxicity induced by TCE. RESULTS: Compared with control, Zebra fish embryos exposed to TCE showed a significant increase in heart defects, and the main phenotypes were abnormal atrioventricular ratio, looping defects and pericardial edema. The results of microarray profiling showed that the expressions of genes related to Wnt signaling pathway were affected significantly. The results of qPCR further confirmed that TCE inhibited the expressions of Wnt pathway target genes Axin2, Sox9b and Nkx2.5(P＜0.05). Wnt agonist CHIR reduced the TCE-induced cardiac malformation rate significantly, while the addition of Wnt antagonist XAV markedly enhanced the cardiac developmental toxicity of TCE. CONCLUSION Exposure to TCE leads to heart malformation in zebrafish embryos. Wnt signaling pathway may be involved in the cardiac developmental toxicity induced by TCE.
Animals ; Gene Expression Regulation, Developmental ; drug effects ; Heart ; drug effects ; embryology ; Transcriptome ; Trichloroethylene ; adverse effects ; Wnt Signaling Pathway ; drug effects ; Zebrafish

With the expanded application of heavy metal cadmium, soil cadmium pollution is more and more serious. In this study, using Salix matsudana as a phytoremediation candidate, we observed changes of gene expression and metabolic pathway after 1, 7 and 30 days under 2.5 mg/L and 50 mg/L cadmium stress. The result of transcriptome sequencing showed that we obtained 102 595 Unigenes; 26 623 and 32 154 differentially expressed genes (DEG) in the same concentration and different stress time; 8 550, 3 444 and 11 428 DEG with different concentrations at the same time; 25 genes closely related to cadmium stress response were screened. The changes of genes expression (such as metallothionein, ABC transporter, zinc and manganese transporter) depended on both concentration of cadmium and exposure time. The expression of several genes was obviously up-regulated after cadmium stress, for example 3,6-deoxyinosinone ketolase (ROT3) in brassinolide synthesis pathway and flavonoid synthase (FLS), flavanone-3-hydroxylase (F3H) in the synthesis pathway of brassinolide. In addition, GO analysis shows that GO entries were mainly enriched in metabolic processes including cellular processes, membranes, membrane fractions, cells, cellular fractions, catalytic activation and binding proteins in response to cadmium stress, whose number would increase along with cadmium concentration and exposure time. The reliability of transcriptome information was verified by qPCR and physiological experimental data. Response mechanisms of S. matsudana after cadmium stress were analyzed by transcriptome sequencing, which provided theoretical guidance for remediation of cadmium pollution in soil by S. matsudana.
Biodegradation, Environmental ; Cadmium ; toxicity ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; drug effects ; Plant Proteins ; genetics ; Reproducibility of Results ; Salix ; drug effects ; genetics ; Stress, Physiological ; genetics ; Transcriptome ; drug effects

OBJECTIVETo investigate the effect of 1,2,3,4,6,7,8,9-octachlorodibenzo-p-dioxin (OCDD) on the testicular gene expression profile in the testis of mice.

METHODSTwenty male C57BL/6j mice were randomly divided into normal control group (fed with maize oil) and 3 OCDD groups treated with OCDD by gavage for 30 days at low-, moderate-, and high doses of 1.25×10(-6), 1.25 ×10(-5), and 1.25×10(-4) g/mL, respectively (8 mL/kg daily). The testicular gene expression profiles of the mice were investigated using gene chip technique and compared between OCDD-exposed groups and the control group.

RESULTSCompared with the control group, the mice in low-dose OCDD group showed 1133 differentially expressed genes, including 659 up-regulated and 474 down-regulated ones; in the moderate-dose OCDD group, 978 genes were differentially expressed, including 487 up-regulated and 491 down-regulated ones; in the high-dose group, 895 genes were differentially expressed, including 424 up-regulated and 471 down-regulated ones.

CONCLUSIONThe effect of sub-chronic exposure to OCDD on testicular gene expression profiles in male C57BL/6j mice indicates that the testis is probably the target organ of OCDD.

Animals ; Male ; Mice ; Mice, Inbred C57BL ; Oligonucleotide Array Sequence Analysis ; Polychlorinated Dibenzodioxins ; toxicity ; Testis ; drug effects ; metabolism ; Transcriptome

Panax japonicus is a traditional Chinese medicine,and its principle components have shown certain pharmacological activities for cell damage,aging and cell apoptosis. In order to clarify the pharmacological mechanism and involved metabolic pathways of P. japonicas,the gene expression of Tetrahymena thermophila under P. japonicus treatment was analyzed through high-throughput transcriptome sequencing in this study. Based on the transcriptome analysis,3 544 differentially expressed genes were identified in control group,of which 1 945 genes showed up-regulated expression and 1 599 genes showed down-regulated expression. Under P. japonicas treatment in the experiment group,3 312 differentially expressed genes were screened,of which 1 `493 genes showed up-regulated expression and 1 819 genes showed down-regulated expression. GO enrichment analysis indicated that in control group,the genes in the cells in a series of fundamental biological process were down-regulated,such as DNA replication and protein synthesis; while the signal transduction process and fatty acids oxidizing process were enriched. Whereas in the experiment group,down-regulated genes were mainly enriched in oxidation-reduction,cofactor metabolic process and vitamin metabolic process; up-regulated genes were enriched in signal transduction process and protein modification process. In the analysis using KEGG database,cell cycle pathway was enhanced and autophagy pathway was inhibited under the condition of P. japonicas treatment. Real-time quantitative polymerase chain reaction( RT-qPCR) was used to detect the expression differences between 6 up-regulated and 4 down-regulated genes in related metabolic pathways. The RT-q PCR results and RNA-Seq data were highly correlated and consistent with each other. This study could provide important direction and basis for further study on the mechanism of cell growth regulation with the treatment of P. japonica.
Gene Expression ; Gene Expression Profiling ; Metabolic Networks and Pathways ; Panax ; chemistry ; Plants, Medicinal ; chemistry ; Tetrahymena thermophila ; drug effects ; genetics ; Transcriptome

OBJECTIVEMethylation-specific epigenetic process and gene expression profiles of HeLa cells treated with ultra-high dilutions (HDs) of two plant extracts, Hydrastis canadensis (HC-30) and Marsdenia condurango (Condu-30), diluted 1060 times, were analyzed against placebo 30C (Pl-30) for alterations in gene profiles linked to epigenetic modifications.

METHODSSeparate groups of cells were subjected to treatment of Condu-30, HC-30, and Pl-30 prepared by serial dilutions and succussions. Global microarray data recorded on Affymetrix platform, using 25-mer probes were provided by iLifeDiscoveries, India. Slides were scanned with 3000 7G microarray scanner and raw data sets were extracted from Cel (raw intensity) files. Analyses of global microarray data profile, differential gene expression, fold change and clusters were made using GeneSpring GX12.5 software and standard normalization procedure. Before microarray study, concentration of RNA (ng/μL), RIN value and rRNA ratio for all the samples were analysed by Agilant Bioanalyzer 2100. Reverse transcriptase polymerase chain reaction (RT-PCR) and quantitative RT-PCR were done for analyzing SMAD-4 expression. Fluorescence-activated cell sorting study was further made to elucidate fate of cells at divisional stages. Methylation-specific restriction enzyme assay was conducted for ascertaining methylation status of DNA at specific sites.

RESULTSHDs of HC-30 and Condu-30 differentially altered methylation in specific regions of DNA and expression profiles of certain genes linked to carcinogenesis, as compared to Pl-30. Two separate cut sites were found in genomic DNA of untreated and placebo-treated HeLa cells when digested with McrBC, compared to a single cut observed in Condu-30-treated genomic DNA. SMAD-4 gene expression validated the expression pattern observed in microarray profile. Methylation-specific restriction enzyme assay elucidated differential epigenetic modifications in drug-treated and control cells.

CONCLUSIONHDs triggered epigenetic modifications and alterations in microarray gene expression profiles of many genes associated with carcinogenesis in HeLa cells in vitro.

Cell Cycle ; Cluster Analysis ; DNA Methylation ; Epigenesis, Genetic ; drug effects ; HeLa Cells ; Humans ; Hydrastis ; Marsdenia ; Plant Extracts ; pharmacology ; Transcriptome ; drug effects

OBJECTIVETo study the molecular mechanisms of Curcuma Wenyujin extract-mediated inhibitory effects on human esophageal carcinoma cells.

METHODSThe Curcuma Wenyujin extract was obtained by supercritical carbon dioxide extraction. TE-1 cells were divided into 4 groups after adherence. 100 microL RMPI-1640 culture medium containing 0.1% DMSO was added in Group 1 as the control group. 100 microL 25, 50, and 100 mg/L Curcuma Wenyujin extract complete culture medium was respectively added in the rest 3 groups as the low, middle, and high dose Curcuma Wenyujin extract groups. The effects of different doses of Curcuma Wenyujin extract (25, 50, and 100 mg/L) on the proliferation of human esophageal carcinoma cell line TE-1 in vitro were analyzed by MTT assay. The gene expression profile was identified by cDNA microarrays in esophageal carcinoma TE-1 cells exposed to Curcuma Wenyujin extract for 48 h. The differential expression genes were further analyzed by Gene Ontology function analysis.

RESULTSCompared with the control group, MTT results showed that Curcuma Wenyujin extract significantly inhibited the proliferation of TE-1 cells in a dose-dependent manner (P<0.05). The expression level of 88 genes changed with significance, including 66 up-regulation genes and 22 down-regulation genes. Gene Ontology analysis indicated the genes coding for proteins was involved in signal transduction (6), cell cycle (8), apoptosis (14), and cell differentiation (10).

CONCLUSIONSThe Curcuma Wenyujin extract could inhibit the growth of human esophageal carcinoma cell line TE-1 in vitro. The molecular mechanisms might be associated with regulating genes expressions at multi-levels.

Apoptosis ; drug effects ; Carcinoma ; metabolism ; pathology ; Cell Line, Tumor ; Cell Proliferation ; drug effects ; Curcuma ; Esophageal Neoplasms ; metabolism ; pathology ; Gene Expression Regulation, Neoplastic ; Humans ; Plant Extracts ; pharmacology ; Transcriptome

OBJECTIVETo characterize the effect of omeprazole on the spectrum of gene expression in the cultured human umbilical vein endothelial cell (HUVEC) line (EA.hy926), and explore the underlying molecular mechanism.

METHODSAffymetrix U133 plus2.0 oligonucleotide microarray was used to detect the alteration in the gene expression profiles induced by 1×10(-5) mol/L omeprazole in HUVECs. Real-time PCR was employed to verify the results of selected differentially expressed genes, and Western blotting was performed to test the expression levels of the related proteins.

RESULTSA total of 282 genes were found to show at least 1.5-fold changes in EA.hy926 cells after treatment with omeprazole for 48 h, including 236 up-regulated and 46 down-regulated ones. These genes were involved in the regulation of transcription, inflammatory response, immune response, cell adherence, anti-apoptosis, and signal transduction.

CONCLUSIONOmeprazole modulates the function of endothelial cells by regulating the gene expression profiles of multiple pathways.

Cell Line ; Computational Biology ; Human Umbilical Vein Endothelial Cells ; drug effects ; Humans ; Oligonucleotide Array Sequence Analysis ; Omeprazole ; pharmacology ; Transcriptome ; drug effects

OBJECTIVE: To explore and analyze the the expression change of miRNA associated with oral submucous fibrosis (OSF) treated by the Salvia combined with law-dose prednisolone. METHODS: Ten pairs of tissues from patients with typical early or advanced stage clinical pathological features of OSF and their paired normal tissues (internal control), were selected respectively. The miRNA expression profiles between the OSF and its paired controls were compared by the Affymetrix analysis. The primary normal oral mucous cells were cultured in arecoline (50 μg/mL) for 3, 6, 12 d (0 d ser ved as cont rol), and the primary OSF-fibroblast cells were cultured with Salvia (90 mg/mL) combined with low-dose prednisolone for 12, 24, 36 h (0 h served as control). The differential expression of miRNA was detected. RESULTS: Arecoline induced the expression changes of miRNAs in normal mucosal cells. Salvia combined with low doses of prednisolone reversed the related miRNA expression. CONCLUSION MiRNAs play an essential role in the occurrence and development of OSF. Salvia combined with low-dose prednisolone can reverse the expression of related miRNAs in OSF cells.
Arecoline ; Cells, Cultured ; Coculture Techniques ; Fibroblasts ; cytology ; drug effects ; Humans ; MicroRNAs ; metabolism ; Mouth Mucosa ; cytology ; drug effects ; Oral Submucous Fibrosis ; metabolism ; Prednisolone ; pharmacology ; Salvia ; chemistry ; Transcriptome

The bursa of Fabricius (BF) is the acknowledged central humoral immune organ in birds. Bursal septpeptide II (BSP-II) is an immunomodulatory bioactive peptide isolated from BF. To understand the effects of BSP-II on immune induction, gene expression profiles of hybridoma cells treated with BSP-II were evaluated. Pathway analysis showed that regulated genes were involved in cytokine-cytokine receptor interactions, T cell receptor signaling pathway, and pathway in cancer. It was observed that BSP-II reduced tumor cells proliferation and stimulated p53 expression. These results indicate potential mechanisms underlying the effects of the humoral immune system on immune induction, including antitumor activities. Our study has provided a novel insight into immunotherapeutic strategies for treating human tumors.
Animals ; Antineoplastic Agents/*pharmacology ; Avian Proteins/*pharmacology ; Bursa of Fabricius/immunology ; Cell Proliferation/drug effects ; Chickens/*immunology ; Hybridomas/drug effects ; Immunologic Factors/*pharmacology ; Oligonucleotide Array Sequence Analysis/veterinary ; Signal Transduction/*drug effects ; *Transcriptome