Objective To explore the microRNA （miRNA） expression changes and related miRNA characteristics of colorectal cancer （CRC） with hepatic metastasis by miRNA microarray. Methods The fresh specimens of primary CRC were collected in 10 patients during operation， which with hepatic metastasis or not. miRNA microarray analysis was performed to compare the miRNA expression levels in two groups. The different expression levels of miRNA were validated by quantitative real-time PCR analysis. Results A total of six dysregulated miRNAs were identified in the CRC patients with hepatic metastasis comparing with CRC patients without hepatic metastasis， including 3 up-regulated miRNAs （miR-224， miR-1236， and miR-622） and 3 down-regulated miRNAs （miR-155， miR-342-5p， and miR-363）， and the quantitative real-time PCR result of miR-224 consisted with the microarray finding. Conclusions miR-224 may be involved in the process of CRC with hepatic metastasis pathogenesis. miR-224 would be a research direction on a new biomarker or therapic method in CRC with hepatic metastasis.
Objective To determine the application values of gene chip technique in cardiovascular surgical clinical and research work. Microarray for gene expression profiles was used to screen out the differentially expressed genes during cardiopulmonary bypass(CPB) in peripheral blood mononuclear cell. By doing these, it was hoped that some clues in inflammatory response during CPB could be found out. Methods The patients’ oxygenated bloods were drawn immediately before onset and termination of CPB. Peripheral blood mononuclear cell (PBMC) were obtained from heparinised blood by Ficoll gradient centrifugation. The differentially expression was measured using BD AtlasTM cDNA Expression Arrays. The candidate genes were corroborated by semiquantitative reverse transcriptionpolymerase chain reaction (RT-PCR). Results Gene chip technique was successfully used in CPB study. The gene expression profiles of cytokines of PBMC during CPB were screened out. Interleukin 6 and Wnt5a were the differentially expressed genes. But the validity using semiquantitative RT-PCR found no statistically difference(P=0.888,0.135). Conclusion Microarray technique has positive application values in the study of cytokines during CPB. cDNA microarray for gene expression profiles can primarily screen out differentially expression genes during CPB. These genes may be engaged in inflammation and other pathophysiological reactions during CPB. PBMC is not the major source of cytokines during CPB.
ObjectiveTo study the mechanism of the effect on invasion and metastasis of colorectal cancer by down-regulating c-Met gene.Methodsc-Met genes were knocked down in SW480 cells, differential genes were screened by gene chip, functional cluster analysis of differential genes was carried out, and IPA was used to analyze the interaction network of cell signal pathway and related differential genes, as well as the ralationship between related genes and upstream regulatory molecules. The related genes in the suppressed signal pathway were selected for qPCR verification.ResultsAfter knockdown of c-Met, the number of up-regulated genes and down-regulated genes in SW480 cells was 399 and 286, respectively. Cluster analysis showed that c-Met knockdown had a great effect on the gene expression level of SW480 cells, IPA pathway analysis showed that HGF signaling pathway was suppressed, and after c-Met knockdown, IPA interaction network suggested that AKT2, PIK3CA, and MAP2K4 in HGF pathway were down-regulated, and qPCR verified that the above genes were also down-regulated, which was consistent with the results of microarray.Conclusionc-Met may affect the invasion and metastasis of colorectal cancer through the regulation of AKT2, PIK3CA, and MAP2K4 in HGF pathway.
Objective To determine the effect of insulin-like growth factor-1 (IGF-1) on angiogenesis in mouse breast cancer model of lower and normal serum IGF-1 levels after using angiogenesis inhibitor ginsenoside Rg3 （GS Rg3）. Methods The breast cancer models were established in control mice and liver specific IGF-1 deficient (LID) mice by feeding DMBA and were treated with GS Rg3. Vascular endothelial growth factor (VEGF) and F8-RAg were detected by immunohistochemical method in breast cancer tissues. IGF-1 gene and angiogenesis relating genes were detected by gene chip in breast cancer and normal breast tissue. Results The incidence rate of breast cancer in LID mice was lower than that in control mice (P＜0.05). VEGF expression and microvessel density of LID mice were lower than those in control mice (P＜0.05). Compared to the control mice, IGF-1, FGF-1, TGF-β1 and HGF genes were increased, and FGFR-2, PDGF-A and PDGF-B genes were decreased in breast cancer of LID mice. After GS Rg3 treatment, VEGFa, EGF, EGFR, PDGF-A and FGFR-2 genes were increased, IGF-1 and TGF-β1 genes were decreased in breast cancer of LID mice compared with the control mice. Conclusion IGF-1 may be involved in mouse breast cancer progression and associated with the growth of blood vessels. Angiogenesis inhibitor may play an antitumor role by IGF-1 and TGF-β1.
Objective To explore the pathogenesis of the level of gene and therapeutic target genes associated with intestinal obstruction by analyzing the differential expression gene. Methods The gene expression data that came from public database gene expression omnibus （GEO） which provided adhesion formation’ gene expression data on 1， 3， 7，and 14 days after operation （n=8） and normal intestinal tissues’ gene expression data （n=2） of mouse were collected. The gene function and differential expression of genes were analyzed by using gene ontology （GO） and significance analysis of microarray （SAM）. Results There were a lot of response stimulated up-regulation of gene expression when occurrence of adhesion， and the products of these genes were distributed on cell membrane. The analysis results of gene expression at different time point after operation showed that expression up-regulated of Hmgcs 2 gene occurred on 3-14 days ofter operation and expression up-regulated of Stxbp 5 gene occurred on 14 days ofter operation. Conclusions The adhesion formation may be closely associated with the genes of response to stimulus and the gene product in membrane. The Hmgcs 2 and Stxbp 5 genes may be closely associated with the occurrence of other diseases which induced by adhesion formation.This provides a basis for the discovery of potential therapeutic targets.
Abstract： Objective To study the difference of gene expression profile of bone marrow mesenchymal stem cells （MSCs） cultured in vitro from coronary heart disease patient with or without diabetes mellitus by Affymetrix Gene array. Methods One male patient at age of 53 years with coronary heart disease and diabetes mellitus was included in this study with the diagnosis of coronary heart disease and type 2 diabetes mellitus. Another male patient at age of 51 years with coronary heart disease without diabetes mellitus was also included in this study with the diagnosis of coronary heart disease. MSCs of the two patients were isolated and purified by the methods of density gradient centrifugation with lymphocyte separation medium for human and adherent filtration. The MSCs expression profile of cytokines and signal transduction genes were examined by Affymetrix gene array. Results There were 27 functional protein genes expression in the patient with coronary heart disease and diabetes mellitus relating to cell apoptosis, cytokine, and signal transduction. Among them, the expression of 13 functional genes, including TNFRSF10B, TNFRSF21, NGF, CAV2, ITGA8, TNS1, ITGA2, AKT3, MBP, MAP2, INHBA, FST, PLA2G5, increased significantly in the patient with coronary heart disease and diabetes mellitus. However, the expression level of 14 genes, including EPR1, BIRC5, HELLS, BCL2, HGF, CASP1, SEPP1, ITGA9, MAP2K6, RUNX3, TGFBR2, RUNX2, CTNNB1, CDC42, decreased significantly. Conclusion The gene expression profile of bone marrow MSCs from coronary heart disease patient with diabetes mellitus is significantly different from the patient with coronary heart disease patient without diabetes mellitus.
DNA microarray has become an essential medical genetic diagnostic tool for its high-throughput, miniaturization and automation. The design and selection of oligonucleotide probes are critical for preparing gene chips with high quality. Several sets of probe design software have been developed and are available to perform this work now. Every set of the software aims to different target sequences and shows different advantages and limitations. In this article, the research and development of these sets of software are reviewed in line with three main criteria, including specificity, sensitivity and melting temperature (Tm). In addition, based on the experimental results from literatures, these sets of software are classified according to their applications. This review will be helpful for users to choose an appropriate probe-design software. It will also reduce the costs of microarrays, improve the application efficiency of microarrays, and promote both the research and development (R&D) and commercialization of high-performance probe design software.
ObjectiveThrough the analysis of gene enrichment in gastric cancer samples, the changes of RNA alternative splicing and related molecular mechanisms were explored.MethodsThe pathological samples of three cases of gastric cancer patients and adjacent tissues were obtained clinically, and the data were obtained by cell culture, protein quantitative labeling, gene chip detection, high-throughput sequencing, etc. GO enrichment was performed on samples by DAVID and other network software, KEGG pathway analysis yielded relevant information for screening for variable splicing of differential genes.ResultsA total of 605 genes with individual ENSG IDs consistent with the gene identification of the ENSEMBL database were screened, and the gene levels of cancer tissues and adjacent tissues were compared. There were 411 non-differentiated genes, 119 differentially up-regulated genes, and 75 differentially down-regulated genes. A total of 69 differentially spliced genes were screened out. Functional annotation and pathway analysis revealed that the detection genes were mainly concentrated in molecular metabolic processes, cell migration, extracellular matrix tissue, blood coagulation, cell matrix adhesion, signal transduction, negative apoptosis regulation, angiogenesis, platelet activation, complement system, adipokines signaling pathway, peroxisome, cancer pathway, transforming growth factor (TGF) signaling pathway, axon guidance, cell cycle, etc.ConclusionThere are a large number of differentially spliced genes in gastric cancer tissue samples, and the difference in expression due to changes in splice sites may play an important role in the development of gastric cancer.