A bioinformatics analysis of acute pancreatitis based on gene expression microarray and drug screening / 临床肝胆病杂志

ObjectiveTo screen out differentially expressed genes (DEGs) and related candidate therapeutic drugs for acute pancreatitis (AP) using the bioinformatics method. MethodsHigh-throughput microarray datasets (GSE109227 and GSE65146) associated with AP in mice were downloaded from gene expression omnibus, and GEO2R was used to screen out DEGs. Database for Annotation, Visualization and Integrated Discovery was used to perform gene ontology and pathway enrichment analysis. Protein-protein interaction (PPI) was established in String database and visualized by Cytoscape, and then subnetwork modules and hub genes were screened out. The microRNAs associated with the hub genes were predicted and candidate drugs were screened out using Comparative Toxicogenomics Database (CTD). ResultsA total of 130 upregulated and 16 downregulated DEGs were screened out in the high-throughput microarray datasets GSE109227 and GSE65146. DEGs were mainly involved in the biological processes such as inflammatory response, neutrophil chemotaxis, tumor necrosis factor-mediated cellular response, and positive regulation of gene expression, and they were also involved in the signaling pathways of extracellular matrix-receptor interaction, regulation of actin cytoskeleton, leukocyte transendothelial migration, and focal adhesion. A total of 12 hub genes and 6 subnetwork modules were screened out in the PPI network. The microRNAs including miR-199a-5p and miR-1-3p might regulate the post-transcriptional regulation of key genes. Genistein, resveratrol, and quercetin which were screened out from CTD database could reduce the expression of key genes. ConclusionRelated genes screened out by the bioinformatics method may play an important role in the development of AP and can be used as the basis for drug screening.

Identification of differentially expressed genes and pathways in lipoprotein lipase gene heterozygous knockout mice through gene microarray analysis / 上海交通大学学报（医学版）

Objective • To screen the differentially expressed genes (DEGs) and pathways in the islet tissues of lipoprotein lipase (Lpl) gene heterozygous knockout (Lpl+/-) mice and wild type (WT) mice, and explore the molecular mechanism of pathogenesis of type 2 diabetes mellitus (T2DM) mediated by lipotoxicity. Methods • The islets of Lpl+/- mice and WT mice were isolated and purified. DEGs were screened by gene microarray analysis. Gene Ontology (GO) function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs were performed. The expressions of key genes were verified by quantitative real-time PCR (qPCR). Results • A total of 187 DEGs were identified. GO functional analysis and KEGG pathway analysis showed that DEGs were mainly involved in the biological processes such as immune cell proliferation and differentiation, inflammatory signaling pathways and cell adhesion. Among the top 10 DEGs screened from Lpl+- mice and WT mice, gremlin 1 (Grem1) gene was closely related to the function of islet β cells, while the result of qPCR was consistent with that of gene microarray analysis. Conclusion • Multiple signaling pathways are involved in the process of T2DM mediated by lipotoxicity, which may lead to the dysfunction of islet β cells by inhibiting Grem1 expression.

Analysis of LncRNAs and mRNAs expression profiles in ovarian epithelial cancer cell lines by gene microarray / 临床检验杂志

Objective To Analyze the expression profiles of LncRNAs and mRNAs in ovarian epithelial cancer cell lines by gene mi-croarray, and then provide experimental evidences for investigating the function of LncRNAs associated with ovarian cancer. Methods The differentially expressed LncRNAs and mRNAs in ovarian epithelial cancer cell lines, such as A2780, HO8910 and SKOV3, and ovarian epithelial cell line HOSEpiC were analyzed by gene microarray. The differentially expressed mRNAs were further performed the KEGG pathway enrichment analysis. The expression levels of six candidate LncRNAs, which had significant difference between the o-varian epithelial cancer cell line and the ovarian epithelial cell line, were further verified by qRT-PCR. Results There were 227 up-regulated LncRNAs and 483 down-regulated LncRNAs in A2780, HO8910 and SKOV3 cell lines. The differentially expressed mRNAs in A2780, HO8910 and SKOV3 cell lines were mainly enriched in the tumor-related pathways such as PI3K-AKT, mTOR and TNF-α( P<0.05) . The expression levels of PTPRG-AS1, CCNT2-AS1, XLOC 009869 and LINC01138 in ovarian epithelial cancer A2780, SKOV3 and OVCR3 cell lines were up-regulated (P<0.05), while those of RP11-252P19.2 and RP11-744I24.2 in ovarian epithelial cancer A2780, SKOV3, OVCR3 and 3AO cell lines were down-regulated ( P<0.05) . Conclusion The differentially expressed LncR-NAs and mRNAs in ovarian epithelial cancer cell lines may be obtained by gene microarray, and the differentially expressed mRNAs are associated with the tumor-related pathways such as PI3K-AKT, mTOR and TNF-α, which may provide new targets for the diagnosis and treatment of ovarian cancer.

Study on expression profile of long non-coding RNA in chronic thromboembolic pulmonary hypertension / 中华胸心血管外科杂志

Objective To investigate the aberrant expression of long non-coding RNA(lncRNA) in chronic thromboembolic pulmonary hypertension,and explore the lncRNA role in pathogenesis of CTEPH.Methods A total of 5 pulmonary artery endarterium tissue of CTEPH patients and 5 pulmonary artery endarterium tissue of healthy controls were collected.Using high-throughput gene microarray technology to detect two groups of lncRNA and mRNA expression spectrum,build lncRNA-mRNA express network,Pathway and GO analysis to explore the gene function.Results Differential expression of 185 lncRNA was observed in the CTEPH tissues compared with healthy control tissues.Further analysis identified 464 regulated enhancerlike lncRNA and overlapping,antisense or nearby mRNA pairs.Coexpression networks were subsequently constructed and investigated.The expression levels of the lncRNA,NR_036693,NR_027783,NR_033766 and NR_001284,were significantly altered.Gene ontology and pathway analysis demonstrated the potential role of lncRNA in the regulation of central process,including inflammatory response,response to endogenous stimulus and antigen processing and presentation.Conclusion Differentially expressed lncRNA may exert a partial role in CTEPH,the results of this study will help in the future about diagnosis and treatment of CTEPH.

Bioinformatic analysis of gene expression of human peripheral blood cells related to radiation injury / 解剖学报

Objective To investigate genes associated with radiation injury and to reveal human peripheral blood cells change during radiation. Methods The microarray data of radiation induced gene expression in human blood were downloaded from the Gene Expression Omnibus (GEO) database and Qlucore Omics Explorer 3.0 software was used to screen differentially expressed genes. Further analysis of differentially expressed genes was conducted by the on-line tools STRING and DAVID. Results Of 94 differentially expressed genes, 31 genes were of co-overexpression and 11 genes were co-underexpressed. These genes were involved in the biological process and molecular function of regulation of apoptosis, regulation of programmed cell death, regulation of cell death, intracellular signaling cascade, response to DNA damage stimulus and regulation of cell cycle. STRING analysis showed that ubiquitin C(UBC), proliferating cell nuclear antigen (PCNA), murine double minute-2 (M DM2) had important roles in the protein-protein interaction network, which participates in p53 pathway. Conclusion UBC, PCNA and MDM2 may be potential therapeutic targets of ionizing radiation exposure through the bioinformatics analysis, which needs further study.

Gene expression profiling of a radioresistant esophageal squamous cancer cell line / 中华放射肿瘤学杂志

Objective To establish a radioresistant esophageal squamous cancer cell line,and to identify the radioresistant genes and mechanisms.Methods The radioresistant KYSE410-res cell line was established by repeated exposure of cell line KYSE410 to radiation.The proliferation and apoptosis of esophageal squamous cancer cells were evaluated before and after radiation.The changes in gene expression of the esophageal squamous cancer cells after radiation were determined by gene microarray and analyzed by group t test.The genes with significant difference in expression after radiation were validated.Results The KYSE410-res cells had significantly enhanced proliferation and anti-apoptosis than the KYSE410 cells (all P＜0.05).The result of gene microarray showed that compared with the KYSE410 cells,the KYSE410-res cells had the expression of 463 and 251 genes upregulated and downregulated by no less than 4 folds,respectively.Those genes with different expression levels after radiation were mainly responsible for cell proliferation,adhesion,signal transduction,angiogenesis,reactive oxygen metabolism,cell damage repair,and the MAPK/ERK signaling pathway.OAS2 and UBD were key proteins in the network.In the KYSE410-res cells,the expression of HLA-DQBI,MMP1,NCAM1,ZNF521,GPC6,SELENBP1,LCN15,and TFPI-2 genes measured by real-time PCR was consistent with that measured by gene microarray.Conclusions Abnormal activation of the MAPK/ERK signaling pathway,upregulated expression of OAS2 and UBD,downregulated expression of TFPI-2,and upregulated expression of MMPs may play a role in radioresistance of esophageal cancer cells.

Preliminary study on expression profiles of plasma circulating microRNAs in patients with sepsis and healthy control people / 实用医学杂志

Objective To identify the circulating miRNAs which can be used to evaluate the diagnosis and prognosis of sepsis by microarray and quantitative real-time PCR,and to predict target genes of miR-519c-5p by bioinformatics analysis. Methods Three sepsis patients,3 septic shock patients and 3 normal controls were enrolled in this study. Plasma RNA was extracted,and was used for hybridized by miRCURY LNATMmicroRNA Array.The signals were scanned and used to conduct differential expression profilings and cluster analysis.Further-more,we performed qRT-PCR to confirm the expression of miRNAs chosen from microarray screening. We used the miRanda and Targetscan databases to predict target genes of the concerned miRNAs and used KEGG database to analyze the related pathways. Results Fifty-seven and 11 miRNAs were observed significantly upregulated in sepsis and septic shock patients,respectively(fold change≥2.0;P<0.05).qRT-PCR results showed that miR-519c-5p was significantly upregulated in patients with sepsis or patients with septic shock compared with the healthy normal controls(P<0.05).Twenty-nine target genes of miR-519c-5p were predicted by the bioinformatics analysis,and 7 potential target genes participate in the sepsis-related pathways.MiR-519c-5p might be a potential positive regulator for the critical cell cycle control gene of MAP2K4,contributing to the vascular endothelial cells apoptosis via MAPK signaling pathway. Conclusions We demonstrated that the plasma level of miR-519c-5p can be used for the diagnosis of sepsis and miR-519c-5p may be a potential therapeutic target for sepsis.

Bioinformatics research of CD44 and epithelial cell adhesion molecule related genes and pathways in colorectal cancer / 中华消化杂志

Objective To investigate genes and involved biological processes closely associated with stem cell markers of colorectal cancer-epithelial cell adhesion molecule (EpCAM) + and CD44+.Methods By the bioinformatics method,with microarray data of colorectal cancer from gene expression omnibus (GEO) database and R2 platform,the genes significantly related with CD44 and EpCAM expression were screened out.The differences in expression of related genes were analyzed on the basis of gender,family history of cancer,alcohol and Dukes stage.The expression of related genes in colorectal cancer was compared with that of other tumors and healthy subjects.At same time,the pathways of the genes and Kyoto encyclopedia of genes and genomes (KEGG) of CD44 and EpCAM significantly related genes were analyzed with gene ontology (GO) and KEGG method.Single factor analysis of variance and Chi-square test of four-fold table with correction for continuity were used for statistical analysis by R2 platform embedded statistical tools.Results The expressions of CD44 and EpCAM were detected in all 315 colorectal cancer samples.A total of 888 and 6 316 genes were screened out which were significantly associated with CD44 and EpCAM expression.CD44 was positively correlated with EpCAM.There was no obvious correlation between the expression of five genes which expressed in all 315 tissues and gender family history of cancer,alcohol and Dukes stage (all P＞0.05).By further compared with the expression in other tumors and tissues,the expressions of two genes solute carrier family 12,member 2 (SLC12A2) and proteome of centriole 1 centriolar protein B (POC1B) in colorectal tumor were significantly higher than that in other tumors (F=289.422、128.456,all P＜0.01),and its expression in colorectal cancer was obviously higher than that in tissues of health subjects (F=349.519、128.456,all P＜0.01).GO analysis indicated there were 15 GO semantics related with both CD44 and EpCAM.The genes related with CD44 and EpCAM were analyzed by KEGG access pathway method,while seven and 10 pathways were found to be statistically significant (all P＜0.01).Conclusions CD44 and FpCAM commonly expressed in colorectal cancer.The genes related with CD44 and EpCAM expression are involved in multiple tumor biological processes.

Study of modified Wuzi-Yanzong prescription's effect on gene expression profile of SAMP8 mice brain based on gene microarray / 中国药学杂志

OBJECTIVE: To study the effect of modified wuzi-yanzong prescription(MWP) on brain gene expression profile in senescence accelerated mouse-prone/8 (SAMP8) mice and detect the mechanism of MWP treating dementia-related diseases. METHODS: Six SAMP8 mice were randomly divided into model group and MWP group on average, meanwhile three senescence accelerated mouse-resistance/1 (SAMR1) mice were chosen as the blank control group. The MWP group was intragastrically intervened by MWP 9 g · kg-1 · d-1, while model group and control goup were given equal volume of sodium carboxyl methyl cellulose, once a day. After 10 d, the mice in experiment were killed and seperated the whole brain. Brain RNA expression was analyzed using Illumina whole genome expression profiles. RESULTS: Compared with the model group, 293 differential genes were screened in the MWP group, including 179 up-regulated genes and 114 down-regulated genes. Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated 17 key targets about differentiation and proliferation of neural stem cells, including Notch pathway, Rap1/B-Raf/ERK pathway and related target proteins; 9 key targets about neural endocrine-immune (NEI) network, including follicle stimulating hormone (FSH), luteinizing hormone (LH), prolactin, thyroid stimulating hormone (TSH), etc. CONCLUSION: The action mechanisms of MWP on brain in SAMP8 mouse involve the regulation of proliferation and differentiation of neural stem cells and NEI network.

Causal genes and pathways analysis of juvenile idiopathic arthritis / 国际生物医学工程杂志

Objective To explore the pathogenesis of juvenile idiopathic arthritis (JIA) and its potential molecular targets.Methods Gene microarray data about JIA was downloaded from Gene Expression Omnibus (GEO) in NCBI.Different expressed genes were identified through bioconductor packages in R programing.The causal genes from the different expressed genes were optimized and replenished by GLAD4U and ToppGene.Functional annotation information of causal genes was carried out by DAVID.Results List of causal genes was obtained as well as their enriched function.Some potential pathways such as Cytokine-cytokine receptor interaction,Jak-STAT signaling pathway,which may be important in the progression of JIA were screened.Conclusions The pathogenesis of JIA,as well as its potential causal genes,can be captured through bioinformatics methods,so it may be used as time and cost saving method in experimental study and clinical application.

Gene expressions of the human intrahepatic cholangiocarcinoma RBE cell line / 中华肝胆外科杂志

Objective To analyze the differentially expressed genes between the NCAM + c-Kit +RBE and NCAM-c-Kit-RBE of intrahepatic cholangiocarcinoma (ICC) cell lines,and to screen out the differentially expressed genes that are related to the stem cell signaling pathways.Methods Magnetic activated cell sorting was used to isolate the NCAM + c-Kit +/NCAM-c-Kit-subset cells,and then Agilent Whole Human Genome Microarray Kit was used to test the difference in gene expressions between the NCAM + cKit + and NCAM-c-Kit-subset cells.The difference in gene expressions related to the stem cell signaling pathways was analyzed by the SAS system.The result of the microarray was further confirmed by RT-PCR.Results The total differentially expressed genes which could be found through gene microarray were 7270 [foldchange(fc) ≥2 or fc ≤0.5].Compared with the NCAM-c-Kit-RBE,3572 genes were upregulated while 3698 genes were downregulated.The differences in gene expressions related to the stem cell signaling pathways were 421 (fc ≥2 or fc ≤ 0.5),among which 231 genes were upregulated while 190 genes were downregulated.Conclusions High-flux microarray could be used to screen out lots of differentially expressed genes between the NCAM + c-Kit + and NCAM-c-Kit-RBE cells.The differences in gene expression in the stem cell signaling pathways could also be further analyzed using the SAS system.

Gene expression profile of continuous mechanical stress-induced osteoblastic differentiation of rat bone marrow stromal cells / 医用生物力学

Objective To evaluate differences in genes expression of rat bone marrow stromal cells (rBMSCs) under continuous mechanical strain by gene microarray technology．Methods rBMSCs were isolated and cultured in vitro. Continuous stresses with amplitude of 10% and frequency of 1 Hz were applied on rBMSCs for 6 hours by Flexercell mechanical loading system to investigate rBMSC gene expression profiles, and quantitative PCR was used to verify gene expression changes related to osteoblastic differentiation. Results Compared with the control group, 1 244 differentially expressed genes were found in mechanical loading group, among which 793 genes were up-regulated, while 451 genes were down-regulated．GO (gene ontology) analysis suggested that differentially expressed genes were mainly involved in multicellular organismal development, cell differentiation, chemotaxis, cell adhesion and so on. Four signaling pathways as Notch, Wnt, FGF and IGF might participate in the regulation of stress-induced osteoblastic differentiation. PCR validation results were consistent with the gene chip results. Conclusions Mechanical stress could induce osteoblastic differentiation of the BMSCs, while several differentially expressed genes screened by gene microarray may attribute to this process.

Relationship between single nucleotide polymorphism in genome of head and neck squamous cell carcinoma tissue and tumor metastasis / 第二军医大学学报

Objective: To screen for the genes associated with metastasis of head and neck squamous cell carcinoma (HNSCC) by studying the specimens of HNSCC. Methods: Eighty HNSCC specimens, including 17 involving the tongue, 13 involving mouth, 14 involving oropharynx, and 36 involving hypopharynx, were subjected to single nucleotide polymorphism chip analysis. The thirty-nine patients with distant metastasis during follow-up were taken as experimental group and the 41 without distant metastasis were taken as controls. Cox regression analysis was used to examine the influence of single nucleotide polymorphism (SNP) on distant metastasis of HNSCC. Results: The results of SNP demonstrated a distinct peak of frequent genomic gain at 11q13. Cox analysis of the array data showed the following results: a relative risk of T allele of rs965l738 as the SNP probe of SHANK2 gene was 3.61(P = 0.003), relative risk of T allele of rs4980690 as the SNP probe of FGF4 gene was 3.63(P = 0.006), relative risk of T allele of rs7929885 as the SNP probe of ANO1 gene was 4.35(P = 0.008), relative risk of T allele of rs687660 as the SNP probe of PPFIA1 gene was 4.24(P=0.011), relative risk of T allele of rs660665l as the SNP probe of ORAOV1 gene was 3.04(P = 0.013), and relative risk of T allele of rs592412 as the SNP probe of CCND1 gene was 4.07(P = 0.013). Conclusion: It is indicated that the following genes at 11q13 can increase the risk of metastasis of HNSCC, including T allele of rs965l738 in SHANK2, T allele of rs4980690 in FGF4, T allele of rs7929885 in ANO1, T allele of rs687660 in PPFIA1, T allele of rs6606651 in ORAOV1, and T allele of rs592412 in CCND1.

Anti-depressant Mechanisms of Wuling Jun Powder by Gene Microarray Analysis / 中国康复理论与实践

@#ObjectiveTo explore the possible mechanisms of Wuling Jun Power by the DNA microarray technique.MethodsAn experimental depression model was established by exposing the mouse to a chronic mild stress procedure. The total RNA was extracted reverse-transcripted and hybrided to the mouse 1-2 cDNA microarray (Clontech). The difference of expression profiles between control model, Wuling Jun powder and fluoxetine-treated groups were analyzed by the Image 2-1 Software.Results130 genes were significantly altered in stress group compared with the control groups. Among them, 116 genes were up-regulated and 14 genes were down-regulated. Meanwhile, 85 genes significantly changed in the Wuling Jun powder treated group with 34 genes up-regulated and 51 genes down-regulated compared with the model groups. For the Fluoxetine-treated group, 133 genes significantly changed with 35 genes up-regulated and 98 genes down-regulated compared with the model groups. These genes were associated with many aspects of life including receptor activity, protein kinases, inflammatory factors, transferrin, neurogenesis and so on.ConclusionMultiple genes were affected by the stress exposure. Altered changes of some genes were normalized by Wuling Jun powder and Fluoxetine treatment. In general, the mechanisms of Wuling Jun powder and Fluoxetine are similar, but also with minor difference.

Mechanism with extremely low frequency electromagnetic field and X-ray irradiation on liver carcinoma BEL-7402 cell lines / 中华放射医学与防护杂志

Objective To investigate the mechanism of extremely low frequency electromagnetic field (ELF-EMF) and X-ray irradiation on liver carcinoma cell lines BEL-7402. Methods Liver carcinoma cell lines BEL-7402 had been incubated with ELF-EMF (100 Hz, 0.7 mT, 30 min, 3 days) after X-ray irradiation at different doses (0, 2, 4, 6, 8,10 Gy). The cells were observed on morphologic changes with scanning electron microscope. Flow cytometry and gene microarray were used to investigate the mechanism of cell apeptosis. Results ELF-EMF plus X-ray induced apoptosis on BEL-7402 was observed under scanning electron microscope.When X-irradiation was 2, 4, 6, 8 and 10 Gy, the apoptosis ratios of combined group and only X-irradiation group were 10.0%, 14.5%, 4.3%, 5.1%, 7.1% and 0.1%, 8.1%, 0.1%, 0.4%, 2.2% (P < 0.05) on flow cytometry. The result of microarray indicated that 1465 genes were up-regulated and 1108 down*regulated in the ELF-EMF plus X-ray group in comparison with the control group. The change rates of 110 apoptosis related genes were above 2 times, which including 71 up-regulated and 39 down-regulated. Gene microarray showed that ELF-EMF and X-ray irradiation had a mainly effect on different gene of apoptosis paths (CDC25 and CHKI, ATM, p38, PTEN, p53, G1/S, Fas, G2/M, Cell Cycle, Apoptosis and Caspase). The same genes of ELF-EMF plus X-ray group were showed 13 in ELF-EMF group and 42 in X-ray group. Conclusions Apoptosis paths were significantly different between ELF-EMF and X-irradiation. ELF-EMF cooperates with X-irradiation on inducing BEL-7402 cell apoptosis.

Screening of the genes related to the development and progression of ESCC / 基础医学与临床

Objective To investigate the differentially expressed genes of primary esophageal squamous cell carci-noma and of normal esophageal mucosa. Methods LCM-GMA-cDNA microarray was used to detect the mRNA from both the primary carcinoma and the corresponding esophageal epithelium in 15 cases of human esophageal squamous cell carcinoma (ESCC). After high-stringent washing, the cDNA microarray was scanned for the fluores-cent signals. Results Among the 886 target genes, 34 genes had significant difference in Ⅰ / Ⅱ and Ⅲ/Ⅳ group. Cell cycle regulators possibly promoting the growth of tumor cells were highly expressed in the early stages of ESCC, whereas adhesion molecules and extracellular matrix-related molecules possibly promoting invasiveness increased in the later stages. Conclusion More than one gene contributed to esophageal cancer. The profiles of gene expression will bring us chance to understanding the molecular mechanism of tumor progression and to support clinical treat-ment.

Preliminary Study of Microarray Gene Expression Profiles in Chronic Congestive Heart Failure due to Rheumatic Heart Disease / 中国循环杂志

Objective:To analyze gene expression profiling of left ventricular myocardium in patients with chronic congestive heart failure(CHF)caused by rheumatic heart disease(RHD)with the normal controls in order to identify CHF associated target genes. Methods:The gene expression profiles of left ventricular myocardium from patients with CHF by RHD and normal controls were obtained from six human whole-genomic oligonucleotide microarrays(Affymetrix HG U133 Plus 2.0 GeneChip). GeneSpring software was used to identify the differentially expressed genes in both groups,and bioinformatic analysis was applied to analyze the target genes associated with CHF. Real-time PCR was carried out to validate the expression of three target genes. Results:We identified 102 target genes associated with CHF which were classified into 7 gene clusters. Microarray results were further confirmed by real time PCR for three genes. ATF3 was markedly down-regulated,IGFBP2 and NPPB were notably up-regulated in the left ventricular myocardium samples from CHF patients. Conclusion:A lot of differentially expressed genes,obtained by using the whole-genomic expression profiling technology,might be a contributory factor for the initiation and progression of CHF and it helpful for the understanding of underlying pathophysiological implications. Further investigation on these genes would provide a strategy to identify genetic markers and molecular events associated with CHF caused by RHD.

Investigation of relevant genes to the pathogenesis and metastasis of osteosarcoma with SBC gene microarray / 中国矫形外科杂志

[Objective]To investigation the relavant genes to the pathogenesis and metastasis of osteosarcoma,and to discuss the significance of gene expression in the pathogenesis and metastasis of osteosarcoma. [Method]Two well-known ATCC osteosarcoma cell lines and an osteoblastic cell line were collected.After the total RNA was extracted,the finally synthesized biotinylated cRNAs were hybridized to SBC arrays.After the design and synthethesis of the primers,four of the differentially expressed genes were then chosen at random to further confirm the array results using the SYBR Green real-time RT-PCR method in freshly collected osteosarcoma specimens and the cell lines.The data analysis depended on the ABI Prism 7300 system.[Result]By an entrance limit of ≥2.0 or ≤0.5,189 up-regulated and 84 dowm-regulated genes which were considerable differentially expressed in the two osteosarcoma cell lines compared with the osteoblastic cell line hfob1.19 were finally detected.Many of the genes were first reported to be related to the pathogenesis of osteosarcoma.The array results were further confirmed by the real-time RT-PCR.[Conclusion]Many genes are involved in the pathogenesis and metastasis of osteosarcoma.It is helpful to apply gene array to find the laws of gene expression and to study the gene-gene interactional relationships in this tumor.

Screening for pathogenesis-related genes of osteosarcoma using gene microarray / 中国肿瘤生物治疗杂志

Objective:To screen for the pathogenesis-related genes of osteosarcoma and to assess their roles for the de- velopment of osteosareoma.Methods:Total RNA was extracted from 3 ATCC osteosarcoma cell lines and an osteoblastic cell line and was used to synthesize biotinylated cRNAs;the latter were hybridized to Affymetrix~(?)GeneChip~(?)U133A ar- rays and a gene with more than 2 folds of change was selected.Ten of the differentially expressed genes were chosen and the primers were designed and the synthesized.Then SYBR~(?)Green real-time PCR(RT-PCR)method was used to detect the expression of the 10 genes in 9 fresh osteosarcoma specimens.ABI Prism 7 000 system was used to analyze the differ- ent expression between osteosarcoma cell line and osteoblastic cell line.Results:We identified 58 up-regulated and 142 down-regulated genes in the 3 osteosareoma cell lines.Many of the genes were firstly reported to be related to the patho- genesis of osteosarcoma.These differentially expressed genes were mainly involved in energy and material metabolism,on- cogene,signal transduction gene,transcription- related genes,cell cycle-related genes,cell apoptosis-related gene,im- mune response gene,tumor suppressor genes,etc.The array results of 10 randomly selected genes were further verified by the RT-PCR in 9 fresh osteosarcoma specimens.Conclusion:Many genes are involved in the pathogenesis of osteosarcoma. Gene microarray can help to discover the genes related to the pathogenesis of osteosarcoma,which may lay a foundation for studying the molecular mechanism of osteosarcom.

Basic Concept of Gene Microarray

The genome sequencing project has generated and will continue to generate enormous amounts of sequence data including 5 eukaryotic and about 60 prokaryotic genomes. Given this ever-increasing amounts of sequence information new strategies are necessary to efficiently pursue the next phase of the genome project-the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip(or gene microarray) technology was developed to efficiently identify the differential expression pattern of independent biological samples. DNA chip provides a new tool for genome expression analysis that may revolutionize many aspects of biotechnology including new drug discovery and disease diagnostics.