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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Detection and analysis of knee osteoarthritis in mice with gene expression profile

When gene expression profile is used for gene detection,the probe on the chip can emit fluorescence with different wavelengths.Under the action of confocal laser scanner,a clear gene change image can be obtained,by which the gene changes of the sample to be tested can be observed directly.First,the knee osteoarthritis(KOA)models of mice are established by the method of collateral ligament and meniscus resection(MLI-OA).Then,Bushen Huoxue formula is given by gavage,and ribonucleic acid(RNA)is routinely extracted and purified.Finally,the gene expression changes of KOA tissues of mice are detected by Agilent SurePrint G3 Mouse GE V2.0 gene expression profile.The results show that Bushen Huoxue formula has significant regulation effect on gene expression of KOA tissue.Among the genes with significant up-regulation effect of Bushen Huoxue formula,there are 56 genes of traditional Chinese medicine(TCM)groups up-regulated more than twice compared with model groups.Among the genes with significant down-regulation effect,there are 119 genes of TCM groups down-regulated more than twice compared with model groups.The experimental results indicate that Bushen Huoxue formula may promote the metabolism of arthritic factors and delay cartilage degeneration to treat KOA by regulating genes that are currently unknown in the pathological process of KOA.

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.

Difference of Gene Expression Profiles between Barrett’s Esophagus and Cardia Intestinal Metaplasia by Gene Chip

The difference of gene expression profile changes in Barrett＇s esophagus （BE） and cardia intestinal metaplasia （CIM） epithelium was studied and the novel associated genes were screened in the early stage by cDNA microarray. The cDNA retro-transcribed from equal quantity mRNA from BE and CIM epithelial tissues were labeled with Cy3 and Cy5 fluorescence as probes. The mixed probe was hybridized with three pieces BiostarH-40s double dot human whole gene chip. The chips were scanned with a ScanArray 4000. The acquired images were analyzed using GenePix Pro 3.0 software. It was found a total of 141 genes were screened out that exhibited differentially expression more than 2 times in all three chips. It was identified that in gene expression profiles of BE, 74 genes were up-regulated and 67 down-regulated as compared with CIM. The comparison between the difference of gene expression profile changes in BE and CIM epithelia revealed that there existed the difference between BE and CIM at gene level. 141 genes with the expression more than two time were probably related to the occurrence and development of BE and the promotion or progress in adenocarcinoma.

Study on the effect of Baiban Ointment on the whole gene expression profile of vulvar sclerosing lichen

Objective:To study the effect of Baiban Ointment on gene expression profile of vulvar lichen sclerosus before and after treatment,and to provide theoretical basis for the early diagnosis and clinical treatment of vulvar lichen sclerosus.Methods:Nine patients with vulvar lichen sclerosus diagnosed pathologically were selected as the study object,and the Baiban ointment was applied locally for 3 months.Gene chip technology was used to detect the vulva skin tissue in the same area before and after treatment,and the peripheral normal skin was used as the normal control group to analyze the change of gene expression profile.FC and P values were used as research indicators,and the standard of differential expression was FC value≥1.5,P value<0.05.The differentially expressed genes were screened,and GO analysis and KEGG database gene pathway analysis were carried out.Results:Compared with the normal control group,there were 22 differentially expressed genes in Group A before treatment,of which 21 were up-regulated and 1 was down regulated;compared with Group B before treatment,there were 23 differentially expressed genes,all of which were up regulated.The differentially expressed genes related to Baiban ointment treatment included TBK1、STAT1、ITGAM、VCAN、PRKACB、PROM1、PLAT、SERPINA1.Go analysis showed that the up-regulated differential genes were mainly concentrated in the extracellular exosome,cytosol,extracellular space,Golgi apparatus and other cellular component,using the biological process such as positive regulation of cell metabolism,signal transduction regulation,cell adhesion,etc.,to play a role in protein binding,enzyme activity regulation and other molecular functions.KEGG signaling pathway showed that the differentially expressed genes were significantly enriched in Toll like receptor signaling pathway,Nod like receptor signaling pathway and Fc RI signaling pathway,all of which were up-regulated signaling pathways.Among them,Toll like receptor signaling pathway and Nod like receptor signaling pathway are most closely related to the disease.Conclusion:Baiban ointment may play a role in regulating metabolism,inflammation and immune response by regulating the expression of related genes,affecting the signal transduction such as Toll like receptor signal pathway.The pathway and the genes screened in this study will provide a direction for the future study of this disease.

Correlation between the gene expression profiles of adenocarcinoma of esophagus and Barrett’s esophagus

Objective： The aim of this study was to investigate the characteristics of gene changes from Barrett＇s esophagus （BE） to esophageal adenocarcinoma by cDNA microarray. Methods： The cDNA retro-transcribed from equal quantity mRNA from esophageal carcinoma and BE tissues as well as control normal epithelium of esophagus which were from one patient with esophageal adenocarcinoma were labeled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with two pieces gene chip respectively. It was scanned by laser scanner Scan Array 4000. The acquired images were analyzed by software GenePix Pro 3.0. Results： A total of 214 genes were screened out which expression levels were more than 2 times in hybridization of esophageal adenocarcinoma vs normal epithelium of esophagus, whereas 90 genes in hybridization of BE vs normal epithelium. A parallel comparison among these two gene profiles showed that a total of 45 genes with 24 downregulation and 21 up-regulation which expression levels were more than 2 times between the BE and the esophageal adenocarcinoma. Among these, there were 27 genes with 18 downregulafion and 9 up-regulation which implicated the tendencies progressing from BE to esophageal adenocarcinoma. Conclusion： These genes or their products which implicate the tendencies can be chosen as indicators of carcinogenesis with high risk index for BE.

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.