Gene Expression Profiling of Meningioma by cDNA Chip

OBJECTIVE: The current progress of the molecular biological study is in the situation of documentation of relation between the tumor development and the gene mutation. We report an analysis of gene expression profiling of meningioma by cDNA chip. METHODS: Meningioma, tumor attached dura and normal dura were obtained during surgery. RNA was extracted from each specimen and cDNA microarray was done. After that, we confirmed the reliability of results from the microarray technique by RT-PCR. RESULTS: We examined the expression of the tumor related gene by cDNA chip. The genes showing two fold changes in the expression were analyzed to find the difference between two groups. The analysis of the tumor and tumor attached dura indicated that the expression of twenty four genes were increased and seventeen genes were decreased in the tumor. The analysis of the gene expression of tumor and normal dura showed increase in twenty seven genes and decrease in thirty one genes. Nine genes in the tumor showed more increase than those in the tumor attached dura and the normal dura. We performed RT-PCR using cytokines to confirm the reliability of the microarray result. CONCLUSION: The cDNA chip contributes as a good laboratory method to check various gene expression of the meningioma and the dura. In the future, the relationship between the expression of IL-1beta, IL-4, IL-6, IL-8, and the function of each gene are required to investigate.

The Study of X Chromosome Inactivation Mechanism in Klinefelter's Syndrome by cDNA Microarray Experiment

To investigate the XIST gene expression and its effect in a Klinefelter''s patient, we used Klinefelter''s syndrome (XXY) patient with azoospermia and also used a normal male (XY) and a normal female (XX) as the control, We were performed cytogenetic analysis, Y chromosomal microdeletion assay (Yq), semi-quantitative RT-PCR, and the Northern blot for Klinefelter''s syndrome (KS) patient, a female and a male control, We extracted total RNA from the KS patient, and from the normal cells of the female and male control subjects using the RNA prep kit (Qiagen), cDNA microarray contained 218 human X chromosome-specific genes was fabricated. Each total RNA was reverse transcribed to the first strand cDNA and was labeled with Cy-3 and Cy-5 fluorescein, The microarray was scanned by ScanArray 4000XL system. XIST transcripts were detected from the Klinefelters patient and the female by RT-PCR and Northern blot analysis, but not from the normal male, In the cDNA microarray experiment, we found 24 genes and 14 genes are highly expressed in KS more than the normal male and females, respectively. We concluded that highly expressed genes in KS may be a resulted of the abnormal X inactivation mechanism.

Gene Expression Profile Analysis of Human Breast Cancer Using cDNA Microarrys / 한국유방암학회지

PURPOSE: The aim of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. METHODS: A total of 7 pairs of breast tumors and control tissues were taken at the time of primary surgery for array analysis. Then, performed microarray experiments in breast cancer tissues with the cDNA microarray spotted 3,063 clones of genes, were analyzed by hierachical clustering. RESULTS: Thirteen genes were over expressed in tumor samples regardless of their histopathological features and ER status, those were including, vitamin A responsive gene, proliferating cell nuclear antigen (PCNA), and signal transducer and activator of transcription 1 (STAT1). Twenty-four genes were down-regulated in tumor sites, those were including, discoidin domain receptor family mamber 2, crystallin alpha B, and myosin light polypeptide kinase. We also identified the differentially expressed genes between ER positive and negative tumors. PCNA, FLJ20500, STAT1, signal recognition particle 9 kD, and proteasome activator subunit 2 were more predominantly expressed in ER negatives. Serine protease 23, vitamin responsive gene, fibronectin 1, and SERPINA1 genes were more highly expressed in ER positive tumors. We further classified the patients according to their gene expression patterns with Cluster program. Clustering results divided patients into two distinct groups, the first group consists of only estrogen receptor (ER) negative tumors and they showed more higher gene expression levels of cell replication and cycle, invasion and metastasis, those considered poor prognosis signature. The other group mostly consists of ER positive tumors. CONCLUSION: These results support the feasibility and usefulness of this systematic approach to studying variation in gene expression patterns in human cancers as a means to dissect and classify solid tumors. We believe, this gene expression profile will outperform all currently available clinical parameters in predicting disease outcome.

The Gene Expression Profile Using cDNA microarray after treatment Arsenic Compound (As2O3, As4O6) in SiHa Cell / 대한산부인과학회잡지

OBJECTIVE: To obtain information on the growth inhibition effect of arsenic compounds and gene expression profiles using cDNA microarray technique in SiHa cell lines. METHODS: We cultured 103 SiHa cell in 96 well plate and we investigated growth inhibition effects using MTT assay and also we performed gene expression profile experiment using 384 cDNA chip in SiHa cell after exposure of arsenics (As2O3, As4O6 - 1 (micro)M) for 48 hrs. RESULTS: Arsenics (As2O3, As4O6) inhibit the growth of SiHa cells (As2O3: 0.5, 1, 2, 3, 4, 5 (micro)M - 9.2, 56, 89, 93, 96, 96%, As4O6: 0.5, 1, 2, 3, 4, 5 (micro)M- 54, 84, 84, 85, 85, 87%) in 4 days culture. As2O3 and As4O6 induced apoptosis in SiHa cells. After exposure of As2O3, 47 genes were changed more than 2 times (eg, thymidylate synthetase, cyclin B1, CDC 20). In case of As4O6, 78 genes were changed more than 2 times (eg, CDC 20, cyclin B1, primase, proliferating cell nuclear antigen). CONCLUSION: we observed arsenic compound (As2O3, As4O6) inhibit the growth of SiHa cell. In gene expression profiling experiment, 78 genes was changed the expression level 2 times more than that of reference RNA after treatment of As4O6 and 47 genes after treatment of As2O3. Through these result, we thought more study need in functional genomics after arsenic treated cervical cancer cells.

Expression Diversity of Quorum-sensing-Related Genes in Pseudomonas aeruginosa / 微生物学通报

One hundred Pseudomonas aeruginosa quorum-sensing-related genes were selected and their primers were synthesized. The fragments of specific sequences which are related QS genes were amplified by PCR. These verified sequences were inserted into the vector pMD-18T for sequencing. These DNA fragments were dotted onto glass slides to make cDNA microarray. Hybridization was performed with cy3/cy5-dCTP labeled probes. The scanning data of early stationary phase and mid-logarithmic phase indicated that 9 genes were up-regulated and 6 genes were down-regulated. Undergoing the different medicines,we took tobramycin as an example to compare the expression diversity. The results confirm that the QS cDNA chip is useful,and may contribute to better understand the mechanism of quorum-sensing,and can help us find the new targets for restraining the growth of Pseudomonas aeruginosa.