Gene expression profiles in response to ΔNp63α overexpression in human cervical cancer cell line SiHa / 安徽医科大学学报

Objective To analyze the gene expression profiles in response to ΔNp63α overexpression, and screen the potential target genes or signal pathways regulated by ΔNp63α. Methods To generate ΔNp63α overexpressed SiHa cells ( SiHa-ΔNp63α) and the control cells ( SiHa-NC) , recombinant lentivirus transfection was performed. Microarray was applied to detect the change of gene expression profiles, and the results were analyzed with bioinfor-matic software. Quantitative real-time PCR was used to validate the expression levels of selected genes. Results Among the 1405 differentially expressed genes which were statistically significant, >1. 5 fold increase or reduce of gene expression, 843 were up-regulated and 562 were down-regulated in SiHa cells with ΔNp63α overexpression. The genes were mostly involved in cell development,cycle regulation, signal transduction, communication, adhe-sion, metastasis and invasion, etc. The involved signal pathways consisted of antigen processing and presentation, cytokine-cytokine receptor interaction, cell adhesion, complement and coagulation cascades, and so on. Conclu-sion The research on the potential target genes or mediated signal pathways regulated by ΔNp63α could be helpful to explain the development of cervical cancer.

Gene-expression profiling of spleen in sepsis rat models / 中华急诊医学杂志

Objective To find out the differences in gene expression of spleen tissue in septic rats by using DNA microarrays.Methods Thirty male Wistar rats were randomly (random number) and equally divided into control group and sepsis group,and septic rat model was induced by cecal ligation puncture (CLP).The rats of control group were only subjected to a simulated operation without CLP.Gene expression profiles were studied by using RatRef-12 gene chip.Rat gene expression profile was showed by using microarray to detect the changes in gene expression pattern of rat spleen tissue after CLP.And subsequently,by using relevant computer software to screen and analyze,the comparison of differences in gene expression between the sepsis group and control group was made.Results Of 22 523 genes,205 differential genes were found between sepsis group and control group,accounting for 0.910％.Among them 98 genes showed up-regulation,with 48 known functional genes,and 107 genes showed down-regulation,with 64 known functional genes.The function of such different genes were associated mainly with apoptosis,inflammation and energy metabolism of spleen cells.Conclusions Splenic dysfunction may be attibuted to the abnormal expression of relevant genes subjected to apoptosis,inflammation and alteration of energy metabolism.It may be the cause of immunosuppression in the later stage of sepsis.

6 Paths of ERK5 signaling pathway regulate hepatocyte proliferation in rat liver regeneration.

Generally, extra-cellular-signal-regulated kinase 5 (ERK5) signaling pathway regulates many physiological activities, such as cell proliferation and cell differentiation. However, little is known about how ERK5 signaling pathway composed of 15 paths participates in regulating hepatocyte proliferation during liver regeneration (LR). In this study, to explore the influence ERK5 signaling pathway upon hepatocytes at gene transcription level, rat genome 230 2.0 array was used to detect expression changes of 75 related genes in isolated hepatocytes from rat regenerating liver. Bioinformatics and systems biology methods were applied to analyze the precise role of ERK5 signaling pathway in regulating hepatocyte proliferation during LR. Results showed that 62 genes were contained in the array and 22 genes were significantly changed. It was found that 6 paths were related to hepatocyte proliferation during rat LR. Among them, paths 3, 6 and 13 of ERK5 signaling pathway modulated cell cycle progression by decreasing the negative influence on ERK5 and paths 3, 4, 8 and 9 by reinforcing the positive influence on ERK5. In summary, the study shows that 22 genes and 6 paths of ERK5 signaling pathway participate in regulating proliferation of hepatocytes in rat LR.

Study on the diferences of gene expression of peripheral blood mononuclear cells between ACCPA+ and ACCPA patients with rheumatoid arthritis / 中华风湿病学杂志

Objective To explore the differences of gene expression of peripheral blood mononuclear cell (PBMC) between the anti-cyclic citrullinated peptide antibody (ACCPA) positive and ACCPA negative patients with rheumatoid arthritis (RA) by microarray analysis.Methods Total RNA was extracted from PBMC of 5 ACCPA positive and ACCPA negative patients with RA,and age-and sex-matched control subjects respectively.Ⅲumina oligonucleotide microarray was used to characterize 47231gene expression profile for each sample.Results Among the target genes,88 differentially expressed genes were identified in RA patients.Fifty-one up-regulated genes and 37 down-regulated genes were found in RA patients compared to those in control subjects (fold change＞1.5).The differential expression of genes were associated with apoptosis,cytokine,signal identification protein,chemotaxis factor etc.There were 20 differential expression genes between the ACCPA positive and ACCPA negative patients with RA,9 up-regulated genes and 11 downregulated genes were found.The differential expression genes were associated with protein biding,,translation control,signal identification protein,cell cycle,metabolism etc.Conclusion There are differential gene expression between the ACCPA positive and ACCPA negative patients with RA.Genes screened from the target such as IFI,KIR,CHI3L1 can provi-de important information for further study and treatment of RA.

Gene expression profiles of peripheral blood mononuclear cells in primary biliary cirrhosis patients / 中华风湿病学杂志

Objective To explore the differentially expressed genes in peripheral blood mononuclear cells of patients with primary biliary cirrhosis and compare it with healthy controls.Methods Peripheral blood mononuclear cells were isolated from 9 primary biliary cirrhosis patients and 9 age and sex matched healthy controls.Total RNA was extracted from peripheral blood mononuclear cells and analyzed by human genome oligonucleotide microarrays (22K).The differences of gene expression and signaling pathway of patients and healthy controls were compared.Results Seventy-nine genes differentially expressed in primary biliary cirrhosis were identified by microarray analysis,in which 21 were up-regulated and 58 were downregulated.The genes were further categorized into 27 signaling pathways,in which 6 pathways were involved in immune regulation and apoptosis:natural killer cell mediated cytotoxicity pathway,toll-like receptor signaling pathway,antigen processing and presentation pathway,cytokine-cytokine receptor interaction pathway,T cell receptor signaling pathway and apoptosis pathway.Conclusion This study has identified that some genes are different in transcription expression in the primary biliary cirrhosis patients.It may provide new clues for the pathogenesis and biomarker studies.

Mycoplasma hyorhinis and Mycoplasma fermentans induce cell apoptosis and changes in gene expression profiles of 32D cells

Infection of mycoplasmas has been linked to various human diseases including arthritis, pneumonia, infertility and cancer. While Mycoplasma hyorhinis and Mycoplasma fermentans have been detected in gastric adenocarcinomas, the mechanisms underlyine the pathogenesis are unknown. In this study, cell growth kinetics, Hoechst 33258 staining, DNA ladder assays, Western blotting analysis and cDNA microarray assays were performed to investigate the roles of M. hyorhinis and M. fermentans during infection of mammalian cells. Our data demonstrated that these mycoplasmas inhibid the growth of immortalised cell lines (32D and COS-7) ane tumor cell lines (HeLa and AGS). In addition, the infection of the 32D cell line with M. hyorhinis and M. fermentans induced compression of the nucleus, degradation of the cell genome and dysregulation of the expression of genes related to proliferation, apoptosis, tumorigenesis, signaling pathway and metabolism. Apoptosis related proteins Bcl-2, Bid and p53 were down-regulated, Fas was up-regulated and Bax was dysregulated in mycoplasma-infected 32D cells. Together, our data demonstrated that infection of mycoplasmas inhibitd cele growts through modification of gene expression profiles and post-translation modification of proliferation and apoptosis related proteins.

PR gene families of citrus: their organ specific-biotic and abiotic inducible expression profiles based on ESTs approach

In silico expression profiles, of the discovered 3,103 citrus ESTs putatively encoding for PR protein families (PR-1 to PR-17), were evaluated using the Brazil citrus genome EST CitEST/database. Hierarchical clustering was displayed to identify similarities in expression patterns among citrus PR-like gene families (PRlgf) in 33 selected cDNA libraries. In this way, PRlgf preferentially expressed by organ and citrus species, and library conditions were highlighted. Changes in expression profiles of clusters for each of the 17 PRlgf expressed in organs infected by pathogens or drought-stressed citrus species were displayed for relative suppression or induction gene expression in relation to the counterpart control. Overall, few PRlgf showed expression 2-fold higher in pathogen-infected than in uninfected organs, even though the differential expression profiles displayed have been quite diverse among studied species and organs. Furthermore, an insight into some contigs from four PRlgf pointed out putative members of multigene families. They appear to be evolutionarily conserved within citrus species and/or organ- or stress-specifically expressed. Our results represent a starting point regarding the extent of expression pattern differences underlying PRlgf expression and reveal genes that may prove to be useful in studies regarding biotechnological approaches or citrus resistance markers.

Phytophthora parasitica transcriptome, a new concept in the understanding of the citrus gummosis

Due to the economic importance of gummosis disease for the citriculture, studies on P. parasitica-Citrus interaction comprise a significant part in the Brazilian Citrus genome data bank (CitEST). Among them, two cDNA libraries constructed from two different growth conditions of the P. parasitica pathogen are included which has generated the PP/CitEST database (CitEST - Center APTA Citros Sylvio Moreira/IAC- Millennium Institute). Through this genomic approach and clustering analyses the following has been observed: out of a total of 13,285 available in the Phytophthora parasitica database, a group of 4,567 clusters was formed, comprising 2,649 singlets and 1,918 contigs. Out of a total of 4,567 possible genes, only 2,651 clusters were categorized; among them, only 4.3 percent shared sequence similarities with pathogenicity factors and defense. Some of these possible genes (103) corresponding to 421 ESTs, were characterized by phylogenetic analysis and discussed. A comparison made with the COGEME database has shown homology which may be part of an evolutionary pathogenicity pathway present in Phytophthora and also in other fungi. Many of the genes which were identified here, which may encode proteins associated to mechanisms of citrus gummosis pathogenicity, represent only one facet of the pathogen-host Phytophthora - Citrus interaction.

The effect of electromagnetic fields on gene expression profiles in bone marrow mesenchymal stem cells / 中华物理医学与康复杂志

Objective To screen for differential expression of genes in bone marrow mesenchymal stem ceils (MSCs) stimulated by electromagnetic fields (EMFs) and to study the mechanism of differentiation of the bone mar- row MSCs induced by EMFs.Methods Mouse bone marrow MSCs were isolated and cultured in vitro.The third- passage cells were stimulated by EMFs,then the total RNA was extracted,purified to cDNA and reversely transcribed to yield a cRNA probe.The cRNA probes from stimulated and control cells were labelled with Cy5 and Cy3,respec- tively.The two samples were hybridized with a mouse oligo microarray,and the hybridization signals were scanned. The reverse transcriptase polymerase chain reaction (RT-PCR) was used to identify the interesting genes:Duspl and Rabl.Results A total of 153 differentially expressed genes were found comparing the stimulated group and the control group.There were 74 up-regulated genes and 79 down-regulated genes in the stimulated group.Semi-quantita- tive RT-PCR confirmed that the Duspl and Rabl mRNA expression levels of the stimulated group were up-regulated. Conclusion The gene expression profiles of the bone marrow MSCs were altered after EMF exposure.The genes are involved in cell proliferation and differentiation,transcription control,metabolism and response to stress.These re- sults provide deeper insight into the mechanism of differentiation of the bone marrow MSCs.

Molecular mechanism study of Trichosanthin induced apoptosis in human cervical carcinoma HeLa cells / 中国药理学通报

Aim To explore effects of TCS on the gene expression profiles of human cervical carcinoma HeLa cells with microarray technique and further investigate its molecular mechanism. Methods RNA from both control and treated HeLa cells were isolated and reversely transcribed to cDNA with the incorporation of cy3 and cy5-labeled dUTP, probes were hybridized with BiostarH-Ⅰ cDNA microarray, chips were scanned and then analyzed by GenePix Pro 3.0 software. Results 78 significantly differently expressed genes were screened out of which up-and down-regulated genes were 62 and 16 respectively. the up-regulated genes were closely related with apoptosis (such as NOP56、TNFSF10、CASP9、DFFB,etc) and the down-regulated genes were associated with the adhesion and interaction between cells (such as COL9A3、LGALS3BP、 MGST3,etc). Conclusion TCS could result in differential expression of multiple genes in HeLa cells, and DNA microarray technique can provide valuable insight into the molecular mechanism of TCS-induced apoptosis.

Effects of hematoperphyrin monomethyl ether on gene expression profiles of human hepatocarcinoma HEPG2 cells with microarray technique / 第二军医大学学报

Objective: To further investigate the molecular mechanism of photodynamic therapy. Methods: We used cDNA microarray technique to explore the gene expression profiles of HEPG2 cells after photodynamic therapy with hematoperphyrin monomethyl ether(HMME) in HEPG2 cells. After treated with HMME for 60 min, the HEPG2 cells were irradiated with laser, and observed by microscope with H E staining. To prepare the probes, mRNA from both control and treated cells were isolated and purified, then reversely transcribed to cDNA with the incorporation of fluorecent labeled dUTP. The probes were hybridized with a cDNA microarray representing the 1 538 genes originated from human hepatocarcinoma cells. The fluorencent signals of Cy3 and Cy5 were scanned and analyzed. Results: After laser irradiation, the HEPG2 cells showed the typical feature of apoptosis. The gene expression profiles were also changed greatly. Among the 1 538 target genes, 389(2.47%) different expression genes were detected. Most of the changed genes (nearly 80%) were down regulated. They were functionally related to cell proliferation cycle, replication, metabolism and so on. Several apoptosis associated genes were detected among those up regulated genes, encoding the key proteins involved in apoptosis signal transduction, such as CCP32,AIF,Mch2. Conclusion: The HMME photodynamic therapy can initiate the apoptosis process of HEPG2 cells, which may be regulated by mitochondial pathway.[