ObjectiveTo explore the mechanism of DDX46 regulation of esophageal squamous cell carcinoma.MethodsPicture signals of fluorescence in gene array were scanned and differential expression of gene in two groups (a DDX46-shRNA-LV group and a control-LV group) were compared by GCOSvL.4 software. These differential expressed genes were analyzed by bioinformatics methods finally, and validated by quantitative real time polymerase chain reaction (qRT-PCR) analysis.ResultsAccording to the screening criteria of fold change ≥2 and P<0.05, 1 006 genes were differentially expressed after DDX46 knockdown, including 362 up-regulated and 644 down-regulated genes. Bioinformatics analysis and gene co-expression network building identified that these differentially expressed genes were mainly involved in cell cycle, proliferation, apoptosis, adhesion, energy metabolism, immune response, etc. Phosphatidylinositol 3-kinase (PI3K) was the key molecule in the network. The results of RT-qPCR were completely consistent with the results of gene microarra.ConclusionBioinformatics can effectively exploit the microarray data of esophageal squamous cell carcinoma after DDX46 knockdown, which provides a valuable clue for further exploration of DDX46 tumorigenesis mechanism and helps to find potential drug therapy.
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.
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.
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.
ObjectiveTo screen for the differentially expressed genes in steroid-induced osteonecrosis of the femoral head (ONFH) by gene microarray. MethodsThe femoral head tissue of ONFH was harvested from 3 patients with steroid-induced ONFH, aged 25, 31, and 38 years, respectively. Normal tissue was harvested from a 26-year-old male remains contributor. HE staining of the specimens was performed for observing the histology manifestation; the total RNA was extracted for measuring the purity; cDNA probe was synthesized by reverse transcription, and then were hybridized as the cDNA microarray for scanning of fluorescent signals and differentially expressed genes in the tissues. ResultsHE staining of normal tissue showed complete unit composed of lamellar bone, continuous and complete lamellar bone with a concentric arrangement around blood vessels, and normal bone cells in the trabecular bone lacuna. In ONFH tissue, adipose tissue increased in the medullary cavity, with increased fat cells filling in the medullary cavity and extruding capillary, and with decreased bone cells in the bone trabecula, which had deeply-stained nuclear chromatin, pyknotic or cracking nucleus, and even bone cells disappeared in the part of the bone lacuna, and trabecular bone became thin, sparse, interrupt, reduced area in visual field/unit. Total RNA extraction electrophoretogram displayed clear bands of 28S and 18S, and the brightness ratio of the 28S:18S was 2:1, indicating good total RNA quality. And 44 genes were differentially expressed, and there were 28 up-regulated genes and 16 down-regulated genes, including cell/organism defense genes, cell structure/motility genes, cell division genes, cell signaling/cell communication genes, cell metabolism genes, gene/protein expression genes, and unclassified genes. ConclusionThe analysis of the gene expression profile of steroid-induced ONFH can provide evidence for the pathogenesis of ONFH.
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 study the differences in gene expression in A549 cells transfected with Forkhead box protein O1(FOXO1),and provide clues to further exploring the mechanism of FOXO1 in acute lung injury. Methods After using TNF-α to stimulate A549 cells,the eukaryotic expression vector GV230-FOXO1 was transfected into A549 cells by using lipofectamine transfection reagent.The RNA was isolated and differentially expressed genes were screened with high-throughout DNA microarray. Results The eukaryotic expression vector GV230-FOXO1 was successfully constructed and verified.High quality mRNA was isolated and prepared for microarray screening,which passed RNA quality control.The DNA microarray data indicated that 317 genes were up-regulated and 237 genes were down-regulated in A549 cells transfected with FOXO1.The function of these differentially expressed genes involved in many aspects,such as proliferation,apoptosis and differentiation. Conclusions Differentially expressed genes in A549 cells transfected with FOXO1 can be successfully screened by using DNA microarray.FOXO1 may influence the progression of the disease by changing the level of cell proliferation,apoptosis and differentiation in acute lung injury.
Objective To investigate the change of immunologic gene expression in cases of colorectal cancer with liver metastasis. Methods The total RNAs were extracted from tumor tissues of original lesions in 16 patients with colorectal cancer， DNA microarray was used to examine the change of immunologic gene expression in colorectal cancer patients with or without liver metastasis. Results Compared with samples without liver metastases， the expressions of 11 immunologic genes obviously down-regulated in the tumor tissues of colorectal cancer patients with liver metastasis， including：carboxypeptidase D；Fc fragment of IgE， high affinityⅠreceptor for gamma polypeptide；Fc fragment of IgG， low affinityⅢa receptor （CD16a）；free fatty acid receptor 2；interleukin 2 receptor gamma；protein tyrosine phosphatase receptor type C；complement factor B；major histocompatibility complex， classⅡ， DM alpha；major histocompatibility complex， classⅡ， DM beta；major histocompatibility complex， classⅡ， DQ alpha 1；granzyme B. The functions involved the growth and activation of immunologic cell， signal transduction， cell apoptotic， cell factors， receptors， complement， apoptotic， and immunogenicity of tumor cell. Conclusions Down-regulation of a various of immunologic gene expression in colorectal cancer patients with liver metastasis inhibits the function of immunology， and tumor cells escaped the destruction of immunology system results in metastasis.