This study aims to clarify host factors of IFN treatment in the treatment of chronic hepatitis B (CHB) patients by screening the differentially expressed genes of IFN pathway CHB patients with different response to interferon (IFN) therapy. Three cases were randomly selected in IFN-responding CHB patients (Rs), non-responding CHB patients (NRs) and healthy participants, respectively. The human type I IFN response RT2 profiler PCR array was used to detect the expression levels of IFN-related genes in peripheral blood monocytes (PBMCs) from healthy participants and CHB patients before and after Peg-IFN-α 2a treatment. The results showed that more differentially expressed genes appeared in Rs group than NRs group after IFN treatment. Comparing with healthy participants, IFNG, IL7R, IRF1, and IRF8 were downregulated in both Rs and NRs group before IFN treatment; CXCL10, IFIT1, and IFITM1 were upregulated in the Rs; IL13RA1 and IFI35 were upregulated in the NRs, while IFRD2, IL11RA, IL4R, IRF3, IRF4, PYHIN1, and ADAR were downregulated. The expression of IL15, IFI35 and IFI44 was downregulated by 4.09 (t = 10.58, P < 0.001), 5.59 (t = 3.37, P = 0.028) and 10.83 (t = 2.8, P = 0.049) fold in the Rs group compared with the NRs group, respectively. In conclusion, IFN-response-related gene array is able to evaluate IFN treatment response by detecting IFN-related genes levels in PBMC. High expression of CXCL10, IFIT1 and IFITM1 before treatment may suggest satisfied IFN efficacy, while high expression of IL13RA1, IL15, IFI35 and IFI44 molecules and low expression of IFRD2, IL11RA, IL4R, IRF3, IRF4, PYHIN1 and ADAR molecules may be associated with poor IFN efficacy.
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 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 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.
Objective Methylprednisolone (MP) is the only active drug for acute spinal cord injury (SCI), but the molecular mechanism is still further studied. To investigate the pathophysiology of SCI and the molecular mechanism of MP in treating SCI. Methods Nine rabbits were randomly divided into 3 groups, weighing (3 100 ± 140) g: sham operation group(group A, n=3), model group (group B, n=3), and drug treatment group (group C, n=3). After laminectomy was performed in3 groups, no treatment was given in group A, and the model of SCI was establ ished with modified Allen’s fall ing strike method in groups B and C at L4; then high-dose MP equivalent with human dose was adopted in group C at 2 hours after SCI and the normal sal ine in group B. All rabbits were sacrificed at 8 hours after SCI, and then the spinal cord tissues about 8 mm long which included the injuried site were obtained. Total RNA was isolated with Trizol one-step method to examine the gene expression profile by using Ogl io technologies with standard operating procedures and qual ity control as recently described respectively. GeneSpring11.0 analyzer software was used to filter potential candidate genes for statistical significance using Welch’s t test, and only genes with P lt; 0.05 and fold change (FC) ≥ 2 were retained for further analysis. Some differentially expressed genes were also verified by RT-PCR to ensure the rel iabil ity of microarray results. Results The SCI model was set up and the samples of spinal cord tissues were acquired successfully at 8 hours after SCI. The qual ify of total RNA from each group met the requirement for the microarray examination and data analysis. These differentially expressed genes involved inflammation, immunity, ion transportation, transcription factors, and so on. The results of genes IL-1α, IL-1β, and defensin 4 (NP-4) by RTPCR were consistent with that of gene-chips. The immuno-related genes included NP-3, NP-4, corticostatin 6, CAP-18, and antimicrobial peptide, which displayed obvious differential expression. Conclusion High-dose MP has protective effects on nervous function by the immunity mechanism, and the main effector may be neutrophil.
ObjectiveTo analyze the expression and prognostic value of PHD Finger Protein 19 (PHF19) in non-small cell lung cancer (NSCLC) based on gene chip data. MethodsThe data about The Cancer Genome Atlas (TCGA) lung cancer patients were downloaded to analyze the expression of PHF19 in lung cancer. The data sets GSE30219 and GSE50081 were downloaded from the Gene Expression Omnibus (GEO), and the patients were screened into the training set and the validation set respectively, thus analyzing the relationship between PHF19 expression, gender, age, tumor clinical stage, pathological type and disease-free survival (DFS), as well as their relationship with overall survival (OS). Gene Ontology (GO)-Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and immune infiltration analysis were performed on PHF19 and co-expression related genes in lung cancer patients through the online database. ResultsThe data from TCGA and GEO showed PHF19 was highly expressed in lung cancer (P<0.001), and PHF19 expression was related to tumor stage. The NSCLC patients in the PHF19 low expression group had longer DFS and OS than those in the high expression group (P<0.05). Multivariate COX regression analysis showed PHF19 was an independent prognostic factor in NSCLC patients (P<0.05). A nomogram drawing to predict the survival rate of lung cancer patients and verifying the C index showed the model has good accuracy. Gene enrichment analysis showed PHF19 high expression is mainly related to the cell cycle, cell nucleus, chromatin, etc. Immune infiltration analysis showed PHF19 is closely related to immune cell infiltration. ConclusionsPHF19 can be used as an indicator to predict the prognosis of NSCLC. PHF19 high expression is an independent predictor of poor prognosis of NSCLC and may be a new target for its treatment.
ObjectiveTo investigate the microRNA (miRNA) expression profile during chondrogenic differentiation of human adipose-derived stem cells (hADSCs), and assess the roles of involved miRNAs during chondrogenesis. MethodshADSCs were harvested and cultured from donors who underwent elective liposuction or other abdominal surgery. When the cells were passaged to P3, chondrogenic induction medium was used for chondrogenic differentiation. The morphology of the cells was observed by inverted phase contrast microscopy. Alcian blue staining was carried out at 21 days after induction to access the chondrogenic status. The expressions of chondrogenic proteins were detected by ELISA at 0, 7, 14, and 21 days. The miRNA expression profiles at pre- and post-chondrogenic induction were obtained by microarray assay, and differentially expressed miRNAs were verified by real-time quantitative PCR (qRT-PCR). The targets of the miRNAs were predicted by online software programs. ResultshADSCs were cultured successfully and induced with chondrogenic medium. At 21 days after chondrogenic induction, the cells were stained positively for alcian blue staining. At 7, 14, and 21 days after chondrogenic induction, the levels of collogen type Ⅱ, Col2a1, aggrecan, Col10a1, and chondroitin sulfate in induced hADSCs were significantly higher than those in noninduced hADSCs (P<0.05). Eleven differentially expressed miRNAs were found, including seven up-regulated and four down-regulated. Predicted target genes of the differentially expressed miRNAs were based on the overlap from three public prediction algorithms, with the known functions of regulating chondrogenic differentiation of stem cells, selfrenewal, signal transduction, intracellular signaling cascade, and cell cycle control. ConclusionA group of miRNAs and their target genes are identified, which may play important roles in regulating chondrogenic differentiation of hADSCs. These results will facilitate the initial understanding of the molecular mechanism of chondrogenic differentiation in hADSCs and subsequently control hADSCs differentiation, and provide high performance seed cells for cartilage tissue engineering.
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.
ObjectiveTo investigate the pathogenesis of atherosclerosis (AS) by detecting different expression genes between normal Wistar rats and rats with atherosclerosis through the technology of gene chip. MethodsThe rats were treated with standard diet with saline injection (control group) or high-cholesterol diet with vitamin D3 injection and balloon injury (model group). Total cholesterol (TC) and triglyeride (TG) in serum were detected 90 days later to ensure the success of establishment of the atherosclerosis model. Abdominal aorta was isolated and stained with HE. Total RNA was isolated from the aorta for gene chip analysis to explore the differential gene expression. ResultsCompared with the control group, the TC and TG level in the model group were highly advanced (P<0.05). AS model was confirmed by pathological observation. Gene chip detection showed that 511 genes were up-regulated and 1 219 ones were down-regulated which were interrelated with lipid metabolism, inflammatory reaction, oxidative stress and apoptosis as well. ConclusionThe expression change with multiple gene in AS suggests that the nosogenesis of AS is adjusted and controlled complicatedly. Intensive study of some important genes will contribute to the prevention and improvement of prognosis of AS.