Effect of Chuanzhifang component (ZGC) on macrophage inflammatory injury based on whole gene expression profile

Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target of this formula on macrophage inflammatory injury at the overall level. Methods: A model of LPS-induced inflammation in RAW264.7 cells was constructed, and the effect of ZGC intervention on the genome-wide expression of inflammatory macrophages 3was examined by gene microarray technology, GO/KEGG enrichment analysis was performed for significantly differentially expressed genes among each group. Results: The results of genome-wide expression profiling microarray analysis showed that the ZGC intervention group upregulated the expression of 5 genes including C4bp and inhibited the expression of 22 genes including Mgat3, Psma6, and Siglecg relative to the LPS model group. KEGG signaling pathway analysis results showed that ZGC mainly acted through cytokine receptor interaction and the C-type lectin receptor signaling pathway. Conclusion: ZGC can interfere with the abnormal expression of 27 genes in inflammatory macrophages, and the related genes may exert corresponding anti-inflammatory effects by affecting cytokine receptor interactions, C-type lectin receptor signaling pathway, and TLR4/ NF-κB signaling pathway.

Expression Profile Changes of Genes Involved in Lipid Metabolism Pathway During Liver Regeneration in Mice

[ Objective ] The aim of the research was to study the expression profile changes of genes involved in lipid metabolism pathway during liver regeneration in mice. [ Method] The CCI4 induced mouse model of liver regeneration was established and the total RNA was isolated from liver tissue of mouse. Then the changes of genes involved in lipid metabolism pathway during different stages of liver regeneration were detected through micro-array chip gene technique and their specific functions were also analyzed. [ Result] Dudng the process of liver regeneration, the expression level of 98 genes involved in lipid metabolism pathway changed, which were divided into eight groups according to change trend. In the mass, the expression of genes was inhibited in the early stage and up-regulated in the late phase. And the gene expression associated with fatty acid synthesis pathway was mainly up-regulated while the catabolic pathway did not change significantly. Most of genes involved in bile acid synthesis pathway were suppressed before 4.5 d and up-regulated after 4.5 d or 7 d. [ Conclusion] During the process of liver regeneration, the genes associated with lipid metabolism are expressed in different trends, and this data should provide a specific range of genes for further studying the regulation effect of lipid metabolism related pathway on liver regeneration.

Genes Expression Profile Difference in Peripheral Blood Between Esophageal Carcinoma Patients and Normal Subjects

Objective： To study the genes expression profile differences in the peripheral blood between esophageal carcinoma patients and normal subjects using the gene chip technique and screen out the esophageal early conceration associated genes. Methods： The total RNA was extracted and purified in the peripheral blood obtained from the patients with esophageal carcinoma and normal subjects. The first strand of cDNA was synthesized through retro-transcription and labeled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with a piece of 4096 double dot human whole gene chip. The acquired image was analyzed by microarrav suite software using a digital computer, and the intensity of ttuorescence signal and its ratio were calculated. Results： A total of 92 genes were screened out and its expression difference was more than 2 times in the peripheral blood between the patients with esophageal carcinoma and normal subjects. Among these, the expression difference of 36 genes was more than 3 times. Two human urokinase plasminogen activator surface receptor （UPAR） genes, 80K-L protein gene, human protein tyrosine-phosphatase gent arid proto-oncogene protein mRNA were significantly up-regulated, while the collagen V type （α-2 gene was markedly down-regulated. Conclusion： 80K-L protein gene, tyrosinephophatase gene, proto-oncogene protein arid the collagen V type α-2 gene might be associated with the ontogenesis, development and its metastasis in the esophageal carcinoma. The UPAR gene may play important roles in the diagnosing the micrometastasis in the peripheral blood of esophageal carcinoma.

Gene expression profile analyses of mice livers injured by Leigongteng

AIM： To analyze the gene expression profiles of mice livers injured by Leigongteng and explore the relationship between the differentially expressed genes and liver damage. METHODS： The experimental mice were randomly divided into a control group and a liver-injured group in which the mice were administrated 33 μγ, of triptolide/ kg per day for 30 d. Liver mRNAs were extracted from animals in both groups and were reverse-transcribed to cDNA with dUTP labeled by different fluorescence （Cy3, Cy5） as hybridization probes. The mixed probes were hybridized with oligonucleotide microarray chips. The fluorescent signal results were acquired by scanner and analyzed with software. RESULTS： Among the 35852 target genes, 29 genes were found to be significantly differentially expressed, with 20 genes up-regulated and 9 genes down-regulated. The reliability of the differentially expressed genes was validated by RT-PCR experiments of 5 randomly selected differentially expressed genes. CONCLUSION： Based on the biological functions of the differentially expressed genes, it is obvious that the occurrence and development of liver damage induced by Leigongteng in mice are highly associated with immune response, metabolism, apoptosis and the cell skeleton of liver cells. This might be important for elucidating the regulatory network of gene expression associated with liver damage and it may also be important for discovering the pathogenic mechanisms of liver damage induced by Leigongteng.

Analysis of gene expression profiles in pancreatic carcinoma by using cDNA microarray

OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarray and detect target genes for further study. METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 cases of moderate-differentiated pancreatic carcinoma were studied by means of cDNA microarray consisting of 18 000 genes. RESULTS: 1484 and 1353 different expressed genes were observed in two cancer samples respectively. We identified 455 genes altered with the same tendency in both samples, including 102 up-regulated and 353 down-regulated genes. There were 274 known genes and 181 unknown genes; 27.8% and 52.0% genes respectively had an expression level in cancer that was 2-fold higher or lower than that in normal samples. Tumor suppressor genes, growth factors and receptor genes, signal conduction genes, transcription factor genes were identified. CONCLUSIONS: cDNA microarray is an efficient and high-throughout method to investigate gene expression profiles in pancreatic carcinoma. MBD1, EDG1 and gene hypermethylation mechanism would play an important role in the pathogenesis of pancreatic carcinoma.

Gene expression profile differences in gastric cancer, pencancerous epithelium and normal gastric mucosa by gene chip

AIM: To study the difference of gene expression in gastric cancer (T), pericancerous epithelium (P) and normal tissue of gastric mucosa (C), and to screen an associated novel gene in early gastric carcinogenesis by oligonudeotide microarray.METHODS: U133A (Affymetrix, Santa Clara, CA) gene chip was used to detect the gene expression profile difference in T, P and C, respectively. Bioinformatics was used to analyze the detected results.RESULTS: When gastric cancer was compared with normal gastric mucosa, 766 genes were found, with a difference of more than four times in expression levels. Of the 766 genes,530 were up-regulated (Signal Log Ratio [SLR]＞2), and 236 were down-regulated (SLR＜-2). When pericancerous epithelium was compared with normal gastric mucosa, 64genes were found, with a difference of more than four times in expression levels. Of the 64 genes, 50 were up-regulated (SLR＞2), and 14 were down-regulated (SLR＜-2). Compared with normal gastric mucosa, a total of 143 genes with a difference in expression levels (more than four times, either in cancer or in pericancerous epithelium) were found in gastric cancer (T) and pericancerous epithelium (P). Of the 143 genes, 108 were up-regulated (SLR＞2), and 35were down-regulated (SLR＜-2).CONCLUSION: To apply a gene chip could find 143 genes associated with the genes of gastric cancer in pericancerous epithelium, although there were no pathological changes in the tissue slices. More interesting, six genes of pericancerous epithelium were up-regulated in comparison with genes of gastric cancer and three genes were down-regulated in comparison with genes of gastric cancer. It is suggested that these genes may be related to the carcinogenesis and development of early gastric cancer.

Monitoring microarray-based gene expression profile changes in hepatocellular carcinoma

AIM: To find out key genes responsible for hepatocarc inogenesis and to further understand the underlying molecular mechanism through investigating the differential gene expression between human normal liver tissue and hepatocellular carcinoma (HCC).METHODS: DNA microarray was prepared by spotting PCR products of 1 000 human genes including 445 novel genes, 540 known genes as well as 12 positive (housekeeping) and 3 negative controls (plant gene) onto treated glass slides. cDNA probes were prepared by labeling normal liver tissue mRNA and cancer liver tissue mRNA with Cy3-dUTP and Cy5-dUTP separately through reverse transcription. The arrays were hybridized against the cDNA probe and the fluorescent signals were scanned. The dataobtained from repeated experiments were analyzed. RESULTS: Among the 20 couple samples investigated (from cancerous liver tissue and normal liver tissue), 38 genes including 21 novel genes and 17 known genes exhibited different expressions. CONCLUSION: cDNA microarray technique is powerful to identify candidate target genes that may play important roles in human carcinogenesis. Further analysis of the obtained genes is helpful to understand the molecular changes in HCC progression and ultimately may lead to the identification of new targets for HCC diagnosis and intervention.

Application of cDNA array for studying the gene expression profile of mature appressoria of Magnaporthe grisea

Appressorium is an infection structure of the phytopathogenic fungus Magnaporthe grisea. Analysis of gene expression profiles ofappressorium development provides insight into the molecular basis of pathogenicity and control of this fungal plant disease. A cDNA array representing 2927 unique genes based on a large EST （expressed sequence tag） database ofM. grisea strain Y34 was constructed and used to profile the gene expression patterns at mycelium and appressorium maturation stages. Compared with mycelia, 55 up-regulated and 22 down-regulated genes were identified in mature appressoria. Among 77 genes, 16 genes showed no similarity to the genome sequences of M. grisea. A novel homologue of peptidyl-prolyl cis-trans isomerase was found to be expressed at low-level in mature appressoria of M. grisea. The results indicated that the genes such as pyruvate carboxylase, phospholipid metabolism-related protein and glyceraldehyde 3-phosphate dehydrogenase involved in gluconeogenesis, lipid metabolism and glycolysis, showed differential expression in mature appressoria. Furthermore, genes such as PTHll, beta subunit of G protein and SGTI involved in cell signalling, were expressed differentially in mature appressoria. Northern blot analysis was used to confirm the cDNA array results.

Gene expression profile of esophageal cancer in North East India by cDNA microarray analysis

AIM： To identify alterations in genes and molecular functional pathways in esophageal cancer in a high incidence region of India where there is a widespread use of tobacco and betel quid with fermented areca nuts. METHODS： Total RNA was isolated from tumor and matched normal tissue of 16 patients with esophageal squamous cell carcinoma. Pooled tumor tissue RNA was labeled with Cy3-dUTP and pooled normal tissue RNA was labeled with Cy5-dUTP by direct labeling method. The labeled probes were hybridized with human 10K cDNA chip and expression profiles were analyzed by Genespring GX V 7.3 （Silicon Genetics）. RESULTS： Nine hundred twenty three genes were differentially expressed. Of these, 611 genes were upregulated and 312 genes were downregulated. Using stringent criteria （P ≤ 0.05 and ≥ 1.5 fold change）, 127 differentially expressed genes （87 upregulated and 40 downregulated） were identified in tumor tissue. On the basis of Gene Ontology, four different molecular functional pathways （HAPK pathway, G-protein coupled receptor family, ion transport activity, and serine or threonine kinase activity）were most significantly upregulated and six different molecular functional pathways （structural constituent of ribosome, endopeptidase inhibitor activity, structural constituent of cytoskeleton, antioxidant activity, acyl group transferase activity, eukaryotic translation elongation factor activity）were most significantly downregulated. CONCLUSION： Several genes that showed alterations in our study have also been reported from a high incidence area of esophageal cancer in China. This indicates that molecular profiles of esophageal cancer in these two different geographic locations are highly consistent.

Differential Gene Expression Profiles in Acute Hepatic Failure Model in Mice Infected with MHV-3 Virus Intervened by Anti-hepatic Failure Compound

Differential gene expression profiles in Balb/cJ mouse model of acute hepatic failure infected with MHV-3 virus intervened by anti-hepatic failure compound （AHFC） and the changes of cytokines regulated by genes were investigated. The Balb/cj mice were divided into AHFC-intervened group and control group randomly. Acute hepatic failure model of Balb/cJ mice infected with MHV-3 virus was established. The survival rate in the two groups was observed. It was found that the survival rate in the AHFC-intervened group and control group was 90% and 50% respectively 48 h after intraperitoneal injection of MHV-3 （P〈0.05）. Before and after the experiment, the cytokines in peripheral blood of the survival mice were determined, and RNA was extracted from survival mouse liver tissue for the analysis of the differential gene expression by a 36 kb mouse oligonuleotide DNA array. In all the genes of microarray there were 332 genes expressed differently in the two groups, in which 234 genes were up-regulated and 78 genes down-regulated. Through clustering analysis, the differential expression of immune related genes, including TNF receptor superfamily, Kctd9, Bcl-2, Fgl2, IL-8, IL-6, IFN-7, TNF-α etc. might be related with the curative effectiveness of AHFC. It was suggested that AHFC can balance the immune state of mouse model of acute hepatic failure infected with MHV-3 virus mainly through regulating the expression of immune related genes, decrease the immune damage and inhibit liver cell apoptosis of mouse acute hepatic failure model obviously so as to increase the survival rate of mouse models of acute hepatic failure.

Gene expression profiles in peripheral blood mononuclear cells of SARS patients

AIM： To investigate the role of inflammatory and anti-vira genes in the pathogenesis of SARS. METHODS： cDNA microarrays were used to screen the gene expression profiles of peripheral blood mononuclear cells （PBMCs） in two SARS patients （one in the acute severe phase and the other in the convalescent phase） and a healthy donor. In addition, real-time qualitative PCR was also performed to verify the reproducibility of the microarray results. The data were further analyzed. RESULTS： Many inflammatory and anti-viral genes were differentially expressed in SARS patients. Compared to the healthy control or the convalescent case, plenty of pro-inflammatory cytokines such as IL-1, TNF-α, IL-8, and MAPK signaling pathway were significantly upregulated in the acute severe case. However, anti-inflammatory agents such as IL-4 receptor, IL-13 receptor, IL-1Ra, and TNF-α-induced proteins 3 and 6 also increased dramatically in the acute severe case. On the contrary, a lot of IFN-stimulated genes like PKR, GBP-1 and 2, CXCL-10 and 11, and JAK/STAT signal pathway were downregulated in the acute severe case compared to the convalescent case. CONCLUSION： Gene expression in SAPS patients mirrors a host state of inflammation and anti-viral immunity at the transcription level, and understanding of gene expression profiles may make contribution to further studies of the SAPS pathogenesis.

Gene expression profile in rat small intestinal allografts after cold preservation/reperfusion

AIM: To determine the changes of gene expression profile in small intestinal allografts in rats after cold preservation/ reperfusion, and to identify the genes relevant to cold preservation/reperfusion injury. METHODS: Heterotopic segmental small bowel transplantation was performed in six rats with a sham operation and they were used as controls. Total RNA was extracted from the allografts (experimental group) and normal intestines (control group) 1 h after cold preservation/ reperfusion, and then purified to mRNA, which was then reversely transcribed to cDNA, and labeled with fluorescent Cy5-dUTP and Cy3-dUTP to prepare hybridization probes. The mixed probes were hybridized to the cDNA microarray. After high-stringent washing, the fluorescent signals on cDNA microarray chip were scanned and analyzed. RESULTS: Among the 4 096 target genes, 82 differentially expressed genes were identified between the two groups. There were 18 novel genes, 33 expression sequence tags, and 31 previously reported genes. The selected genes may be divided into four classes: genes modulating cellular adhesion, genes regulating cellular energy, glucose and protein metabolism, early response genes and other genes. CONCLUSION: A total of 82 genes that may be relevant to cold preservation/reperfusion injury in small intestinal allografts are identified. Abnormal adhesion between polymorphonuclears and endothelia and failure in energy, glucose and protein metabolism of the grafts may contribute to preservation/reperfusion injury. The functions of the novel genes identified in our study need to be clarified further.

Analysis of hippocampal gene expression profile of Alzheimer's disease model rats using genome chip bioinformatics

In this study, an Alzheimer＇s disease model was established in rats through stereotactic injection of condensed amyloid beta 1-40 into the bilateral hippocampus, and the changes of gene expression profile in the hippocampus of rat models and sham-operated rats were compared by genome expression profiling analysis. Results showed that the expression of 50 genes was significantly up-regulated （fold change 〉 2）, while 21 genes were significantly down-regulated in the hippocampus of Alzheimer＇s disease model rats （fold change 〈 0.5） compared with the sham-operation group. The differentially expressed genes are involved in many functions, such as brain nerve system development, neuronal differentiation and functional regulation, cellular growth, differentiation and apoptosis, synaptogenesis and plasticity, inflammatory and immune responses, ion channels/transporters, signal transduction, cell material/energy metabolism. Our findings indicate that several genes were abnormally expressed in the metabolic and signal transduction pathways in the hippocampus of amyloid beta 1 40-induced rat model of Alzheimer＇s disease, thereby affecting the hippocampal and brain functions.

Expression Profile of Metastasis-associated Genes in Esophageal Squamous Cell Carcinoma

The differentially expressed genes between esophageal squamous cell carcinoma （ESCC） with or without lymphatic metastasis were investigated by gene chip, and the lymphatic metastasisassociated genes were screened out. Expression array was used to detect the mRNA from both the primary carcinoma and the corresponding esophageal epithelium in 15 cases of human ESCC. The lymphatic metastasis-associated genes were screened by bioinformatics between ESCC with or without lymphatic metastasis. The results showed that 43 （4. 85 %） genes significantly differed between the ESCC with and without lymphatic metastasis （P〈0.05）, of which 18（2.03 %）were upregulated and 25 （2.82 %） down-regulated. The up-regulated genes were involved in cell adhesion molecules and cell membrane receptors and the down-regulated genes were mostly cell cycle regulators and intracellular signaling molecules. It was suggested that lymphatic metastasis-associated genes were screened by gene chip, which was helpful to understand the molecular mechanism of ESCC lymphatic metastasis and lymphatic metastasis-associated genes might be used as diagnostic markers and therapeutic targets for lymphatic metastasis.

Immune Responses to Trichloroethylene and Skin Gene Expression Profiles in Sprague Dawley Rats

Objective To characterize the immune reaction in SD rats exposed to trichloroethylene （TCE） and to identify the gene expression profiles involved in skin after TCE exposure. Methods Fifteen percent of TCE was injected intradermally into the rat back （100 μL/120 g） at intervals of 7 days. Whole blood was collected 24 h after the fifth or seventh intradermic administration of TCE. The percentages of CD4＋ and CD8＋ of T lymphocytes were measured by a flow cytometer. The concentrations of IFN-gamma and 1L-4 in the serum were semi-quantified by ELISA. Total RNAs of skin samples at 3 h or 24 h after the seventh dose of TCE in SD rats were extracted, and gene expression proftles of these tissues were analyszed by rat toxicology U34 array of Affymetrix. Results Obvious decline of CD4＋ in T lymphocytes was observed in the TCE-administer group. No significant concentration differences in IFN-gamma and IL-4 were found between TCE-treated and control rats. Gadd45a and Mel were significantly up regulated in skin tissue 24 h after TCE exposure. The expression regulation of immune response factors was as active as proteins associated with lipid metabolism and synthesis process in these skin samples of SD rats exposed to TCE. Conclusion T-helper type 1 cells mediate immune response can not be elicited in TCE-treated SD rats, but certain immune disorder can be induced.

THE GENE EXPRESSION PROFILE OF HIGHLY METASTATIC HUMAN OVARIAN CANCER CELL LINE BY GENE CHIP

Objective: To study the gene expression of high metastatic human ovarian carcinoma cell line (HO-8910PM) and to screen for novel metastasis- associated genes by cDNA microarray. Methods: The cDNA was retro-transcribed from equal quantity mRNA derived from tissues of highly metastatic ovarian carcinoma cell line and normal ovarian, and was labeled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with BioDoor 4096 double dot human whole gene chip. The chip was scanned by scanArray 3000 laser scanner. The acquired image was analyzed by ImaGene 3.0 software. Results: By applying the cDNA microarray we found: A total of 323 genes whose expression level were 3 times higher or lower in HO-8910PM cell than normal ovarian epithelium cell were screened out, with 71 higher and 252 lower respectively. Among these 10 were new genes. 67 genes showed expression difference bigger than 6 times between HO-8910PM cell and normal ovarian epithelium cell, among these genes 12 were higher, 55 lower, and two new genes were found. Conclusion: cDNA microarray technique is effective in screening the differentially expressed genes between human ovarian cancer cell line (HO-8910PM) and normal ovarian epithelium cell. Using the cDNA microarray to analyze of human ovarian cancer cell line gene expression profile difference will help the gene diagnosis, treatment and protection.

Analysis of Gene Expression Profile in Lung Adenosquamous Carcinoma Using cDNA Microarray

Gene expression profile of the lung adenosquamous carcinoma was characterized by using cDNA microarray chip containing 4 096 human genes. Among target genes, 508 differentially expressed genes were identified in adenosquamous carcinoma of the lung, 232 genes were overexpressed and 276 genes were underexpressed. Among them, 92 genes are cell signals transduction genes, 34 genes are proto-oncogenes and tumor suppressor genes or cell cycle related genes or cell apoptosis related genes, 29 genes are cell skeleton genes, 28 genes are DNA synthesis, repair and recombination genes, 12 genes are DNA binding and transcription genes. These genes may be associated with the occurence and development of adenosquamous carinome of the lung. Key words lung carcinoma - adenosquamous carcinoma - microarray - gene expression profile CLC number R 734.2 Foundation item: Supported by the National Natural Science Foundation of China (39870305)Biography: YANG Fei(1972-), female, Ph. D candidate, research direction: etiology and pathogenesis of lung cancer.

Verification of gene expression profiles for colorectal cancer using 12 internet public microarray datasets

AIM: To verify gene expression profiles for colorectal cancer using 12 internet public microarray datasets.

Gene expression profile analysis reveals the effect of metformin treatment on HepG2 cells

Metformin is a first-line drug in the fight against type 2 diabetes.In recent years,studies have shown that metformin has some preventive and therapeutic effects on liver cancer,but the effects of metformin on the gene expression of liver cancer cells are not fully known.This study focused on the differences in the gene expression profiles in liver cancer cells treated with or without metformin.A total of 153 differentially expressed genes(DEGs)(FC>2 and q-values<0.001)were found,including 77 upregulated genes and 76 downregulated genes.These DEGs are involved in mitogen-activated protein kinase(MAPK),nuclear factor-kappa B(NF-κB),cell adhesion molecules(CAMs),and leukocyte transendothelial migration signaling pathways.These findings reveal the effects of metformin treatment on gene expression profiles in liver cancer cells and provide new clues for unveiling the mechanism of the antitumor effects of metformin.

Oligomicroarray-based primary study of gene expression profile changes in Barrett’s esophagus

Objective: To analyze the differential expression genes (DEGs) between Barrett’s esophagus (BE) and normal esophagus mucosa and explore the target genes related to the development and progression of BE. Methods: The total RNAs of matched BE and normal esophagus mucosa of BE patients were isolated using one step Trizol method. Matched RNAs were qualified using 10 g/L agarose gel electrophoresis. cRNAs were synthesized, fluorescence labeled and purified after total RNAs were purified. The RNAs of BE and normal esophagus mucosa were hybridized with Agilent oligomicroarray (30 968 probes). The fluorescence intensity features were detected by Agilent scanner and quantified by feature extraction software. Results: (1) The total RNA, reverse transcription product and fluorescence labeled cRNA were all of high quality; (2) There were 142 up-regulated genes and 284 down-regulated genes among 2-fold DEGs. Conclusion: Microarray-based studies are feasible in endoscopically obtained tissues. Many BE-associated genes are screened by the high-throughput gene chip. The development and progression of BE is a complicated process involving multiple genes and multiple procedures, and functional study of these genes may help to identify the key genes or pathways involved in the pathogenesis and development of BE.