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.
Objective To identify genes associated with hepatocellular carcinoma (HCC) as candidate diagnostic markers in a genome-wide scale. Methods The gene expression profiles of 40 pairs of HCC tumor tissue and peripheral non-tumorous liver tissue were analyzed by using gene chip technology.The gene chips were fabricated at the National Cancer Institute (NCI). Each gene chip contained 9 180 genes. The fluorescent targets were prepared by a direct labeling approach using two kinds of fluorescences as following: 100 μg of total RNA from non-cancerous liver tissue was labeled with Cy3-dUTP and 200 μg of total RNA from HCC was labeled with Cy5-dUTP. The targets were mixed together and hybridized with genes on the gene chips. Unsupervised hierarchical clustering analysis was done by CLUSTER and TREEVIEW software using median centered correlation and complete linkage. Results A total of 10 genes were found up-regulated in over 80% of primary tumors comparing with that of their corresponding non-tumorous liver tissues at a two-fold filter with an unsupervised hierarchical clustering algorithm, including protocadherin-alpha 9, ESTs, Homo sapiens cDNA FLJ, KPNA2, RPS20, SNRPE, CDKN2A, UBD, MDK and ANXA2.Conclusion These genes are supposed to be candidates for the diagnosis of HCC. Further investigation of these genes in a large scale of patients with HCC and patients with non-malignant hepatic diseases will be needed to disclose whether they could be used clinically as novel diagnostic tumor markers for HCC.
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.
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.
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.
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.
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.
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 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.