人Ⅰ型基质金属蛋白酶基因真核表达重组质粒的构建

【目的】构建人Ⅰ型基质金属蛋白酶基因 (MMP1)真核表达重组质粒 ,并进行序列分析。【方法】用逆转录聚合酶链反应扩增人Ⅰ型基质金属胶原酶cDNA ,获得目的基因片段 (140 7bp)连接至 pcDNA3载体 ,并转化大肠杆菌DH5α,筛选阳性克隆并鉴定 ,并对片断全长进行DNA序列测定。【结果】所克隆人Ⅰ型基质金属胶原酶cDNA ,含全长MMP1编码区 ,与GeneBank公布序列比较 ,仅 1318位的胞苷酸C突变为腺苷酸A。并成功构建了含有MMP1的真核表达质粒 pcDNA3 MMP1。【结论】以逆转录聚合酶链反应方法成功构建了人Ⅰ型基质金属胶原酶cDNA克隆 ,并获得该基因真核表达质粒pcDNA3 MMP1,从而为下一步抗肝纤维化基因治疗研究提供物质基础。

Expression of heparanase mRNA in anti-sense oligonucleotide-transfected human esophageal cancer EC9706 cells

AIM： To investigate the effed3 of anti-sense oligonucleotides （ASODNs） on mRNA expression of heparanase in human esophageal cancer EC9706 cells. METHODS： One non-sense oligonucleotide （N-ODN） and five ASODNs against different heparanase mRNA sites were transfected into EC9706 cells, then the expression of heparanase mRNA in EC9706 cells was studied by in situ hybridization. RESULTS： The expression of heparanase mRNA could be inhibited by ASODNs.There was no significant difference among five ASODNs （P〉0.05）, but there was a significant difference between ASODNs and N-ODN or non-transfected group （ASODNI： 2.25±0.25, ASODN2： 2.21±0.23, ASODN3： 2.23±0.23, ASODN4：2.25±0.24 vs N-ODN： 3.47±2.80 or non- transfected group： 3.51±2.93 respectively, P〈0.05）. CONCLUSION： The expression of heparanase mRNA in EC9706 cells can be inhibited by ASODNs in vivo, and heparanase ASODNs can inhibit metastasis of esophageal squamous cell carcinoma or other tumors by inhibiting the expression of heparanase.

Cross-species hybridization of woodchuck hepatitis virus-induced hepatocellular carcinoma using human oligonucleotide microarrays

AIM： To demonstrate the feasibility of using woodchuck samples on human microarrays, to provide insight into pathways involving positron emission tomography （PET） imaging tracers and to identify genes that could be potential molecular imaging targets for woodchuck hepatocellular carcinoma. METHODS： Labeled cRNA from woodchuck tissue samples were hybridized to Affymetrix U133 plus 2.0 GeneChips. Ten genes were selected for validation using quantitative RT-PCR and literature review was made. RESULTS： Testis enhanced gene transcript （BAX Inhibitor 1）, alpha-fetoprotein, isocitrate dehydrogenase 3 （NAD＋） beta, acetyI-CoA synthetase 2, carnitine palmitoyltransferase 2, and N-myc2 were up-regulated and spermidine/spermine N1-acetyltransferase was down-regulated in the woodchuck HCC. We also found previously published results supporting 8 of the 10 most up-regulated genes and all 10 of the 10 most downregulated genes. CONCLUSION： Many of our microarray results were validated using RT-PCR or literature search. Hence, we believe that woodchuck HCC and non-cancerous liver samples can be used on human microarrays to yield meaningful results.

Gene Expression Profile Differences in Gastric Cancer and Normal Gastric Mucosa by Oligonucleotide Microarrays

OBJECTIVE To study the difference of gene expression in gastric cancer (T) and normal tissue of gastric mucosa (C), and to screen for associated novel genes in gastric cancers by oligonucleotide microarrays. METHODS U133A (Affymetrix, Santa Clara, CA) gene chip was used to detect the gene expression profile difference in T and C. Bioinformatics was used to analyze the detected results. RESULTS When gastric cancers were compared with normal gastric mucosa, a total of 270 genes were found with a difference of more than 9 times in expression levels. Of the 270 genes, 157 were up-regulated (Signal Log Ratio [SLR] ≥3), and 113 were down-regulated (SLR ≤-3). Using a classification of function, the highest number of gene expression differences related to enzymes and their regulatory genes (67, 24.8%), followed by signal-transduction genes (43,15.9%). The third were nucleic acid binding genes (17, 6.3%), fourth were transporter genes (15, 5.5%) and fifth were protein binding genes (12, 4.4%). In addition there were 50 genes of unknown function, accounting for 18.5%. The five above mentioned groups made up 56.9% of the total gene number. CONCLUSION The 5 gene groups (enzymes and their regulatory proteins, signal transduction proteins, nucleic acid binding proteins, transporter and protein binding) were abnormally expressed and are important genes for further study in gastric cancers.

Expression profiling of gastric cancer samples by oligonucleotide microarray analysis reveals low degree of intra-tumor variability

AIM： Gene expression profiling provides an unique opportunity to gain insight into the development of different types of gastric cancer. Tumor sample heterogeneity is thought to decrease the sensitivity and tumor specificity of microarray analysis. Thus, microdissection and preamplification of RNA is frequently performed. However, this technique may also induce considerable changes to the expression profile. To assess the effect of gastric tumor heterogeneity on expression profiling results, we measured the variation in gene expression within the same gasbic cancer sample by performing a gene chip analysis with two RNA preparations extracted from the same tumor specimen. METHODS： Tumor samples from six intestinal T2 gastric tumors were dissected under liquid nitrogen and RNA was prepared from two separate tumor fragments. Each extraction was individually processed and hybridized to an Affymetrix U133A gene chip covering approximately 18 000 human gene transcripts. Expression profiles were analyzed using Microarray Suite 5.0 （Affymetrix） and GeneSpring 6.0 （Silicon Genetics）. RESULTS： All gastric cancers showed little variance in expression profiles between different regions of the same tumor sample. In this case, gene chips displayed mean pair wise correlation coefficients of 0.94±0.02 （mean±SD）, compared to values of 0.61±0.1 for different tumor samples. Expression of the variance between the two expression profiles as a percentage of “total change” （Affymetrix） revealed a remarkably low average value of 1.18±0.78 for comparing fragments of the same tumor sample. In contrast, comparison of fragments from different tumors revealed a percentage of 24.4±4.5. CONCLUSION： Our study indicates a low degree of expression profile variability within gastric tumor samples isolated from one patient. These data suggest that tumor tissue heterogeneity is not a dominant source of error for microarray analysis of larger tumor samples, making total RNA extraction an appropriate strategy for performing gene chip expression profiling of gastric cancer.

Understanding the transcriptional control of gene expression using ChIP-chip technology

Gene expression profiling using cDNA or high-density oligonucleotide microarray contributes signifi cantly to our understanding on the transcriptome of a given biological condition. Using this technology, huge number of differentially-expressed genes of interest have been identified in a broad range of circumstances. Making sense biologically on these genes using the recently-improved functional annotation and data integration has leveraged our understanding in diseases and their biological mechanisms. However, understanding the codes encrypt- ed in the cis-aeting regulatory regions and gaining insights into the circuitry of functional regulatory networks on the genomic scale will require additional empirical data sets that are capable of revealing the cohorts or regulons of the transcription and the dynamic progression of molecular events responsible for certain biological function.