No abstract available.
DNA, Neoplasm/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/methods ; Urologic Neoplasms/*genetics

OBJECTIVEEstablishment of a gene expression profile associated with differentiation inducing the glioma cells was made possible.

METHODThe expression level of 18 000 genes in glioma cells was evaluated before and after induction with sodium phenyl-butyrate for 2 hours or 6 days by cDNA array technique, with the results proved by multi-dot blot.

RESULTSNinety-eight gene expressions in the glioma cells were changed after the induction, with some genes in transcription and translation systems down-regulated, some oncogenes down-regulated, and some differentiation or apoptosis genes up-regulated. Eighteen unknown EST fragments were changed also.

CONCLUSIONA gene expression profile associated with differentiation-inducing the glioma cells including 98 genes has been established.

Cell Differentiation ; DNA, Neoplasm ; analysis ; Gene Expression ; Gene Expression Profiling ; Glioma ; genetics ; metabolism ; pathology ; Humans ; Oligonucleotide Array Sequence Analysis ; RNA, Neoplasm ; analysis

High-throughput genomic technologies (HGTs), including next-generation DNA sequencing (NGS), microarray, and serial analysis of gene expression (SAGE), have become effective experimental tools for cancer genomics to identify cancer-associated somatic genomic alterations and genes. The main hurdle in cancer genomics is to identify the real causative mutations or genes out of many candidates from an HGT-based cancer genomic analysis. One useful approach is to refer to known cancer genes and associated information. The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. Some cancer gene or mutation databases exist for this purpose, but few specialized tools exist for an automated analysis of a long gene list from an HGT-based cancer genomic analysis. This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, and associated annotations through annotation and browsing functions. With this tool, researchers can classify their candidate genes from cancer genome studies into either previously reported or novel categories of cancer genes and gain insight into underlying carcinogenic mechanisms through a pathway analysis. We show the usefulness of CaGe by assessing its performance in annotating somatic mutations from a published small cell lung cancer study.
Gene Expression ; Genes, Neoplasm ; Genome ; Genomics ; Sequence Analysis, DNA ; Small Cell Lung Carcinoma

No abstract availble.
DNA Mutational Analysis ; Humans ; *Microsatellite Instability ; Neoplasm Staging ; Prognosis ; Stomach Neoplasms/*diagnosis/genetics/surgery

PURPOSE: In advanced gastric cancer, the important prognostic factors are depth of invasion and status of lymph node metastasis, etc. In early gastric cancer, it remains controversial that depth of invasion or lymph node metastasis is corelated to the prognosis. A retrospective analysis of early gastric cancer was performed to evaluate the clinicopathologic features and to know the factors affecting the prognosis. MATERIALS AND METHODS: From January 1981 to May 1997, we experienced 1850 cases of gastric cancer who performed gastric resections. Among them, 371 cases were early gastric cancer (20.1% of all resected gastric cancer cases). We defined 12 variable factors such as sex, age, tumor location, gross type, histologic type, depth of invasion, status of lymph node metastasis, tumor size, DNA ploidy pattem, stage, operation type, and resection type for prognostic factor and analyzed them. RESULTS: Overall five year survival rate was 89.6% and ten year survival rate was 82.0%. The trend of annual incidence in recent nine years showed steady increase from 13.1% in 1988 to 25.7% in 1996. Survival showed no significant correlation with sex, age, tumor location, gross type, histologic type, tumor size, DNA ploidy, resection type. According to univariate analysis, depth of invasion, lymph node metastasis, stage had statistically significant association with prognosis. Among them, lymph node metastasis had an inde- pendent and predominant impact on survival according to multivariate analysis. CONCLUSION: Early gastric cancer appears to show steady increase of annual incidence, and lymph node metastasis appears to be closely related to the prognosis.
DNA ; Incidence ; Lymph Nodes ; Multivariate Analysis ; Neoplasm Metastasis ; Ploidies ; Prognosis ; Retrospective Studies ; Stomach Neoplasms* ; Survival Rate

The necessity of early detection of prostate cancer renewed interest regarding putative premalignant lesions in the tumorigenesis of the prostate. Prostatic intraepithelial neoplasia (PIN) is one potential precursor for prostatic adenocarcinoma. The term PIN has been adopted to replace a wide range of synonyms in the literature that describe potential precursors. PIN is an intraluminal proliferation of the secretory cells lining architecturally benign prostatic ducts and acini that exhibit cytologic atypia. In this review, we discuss the histologic features, the differential diagnosis, the evidence that PIN is a precursor of prostatic carcinoma, and the clinical significance of PIN.
Adenocarcinoma/*pathology ; DNA, Neoplasm/analysis ; Diagnosis, Differential ; Human ; Male ; Precancerous Conditions/*pathology ; Prostatic Neoplasms/*pathology

OBJECTIVETo study the prognostic identification of lymph node negative breast carcinoma by quantitative pathologic technique.

METHODSSeveral morphometrical parameters, DNA content of cell nuclei were detected by means of a quantitative pathologic technique on 102 patients with lymph node negative invasive breast duct carcinoma. The effects of potential prognostic factors of lymph node negative breast cancer patients were assessed by Cox's proportional hazards regression model.

RESULTSDNA index, minimal diameter of nuclei, area of nuclei, maximal diameter of nuclei, and the perimeter of nuclei are important factors to influence the prognosis.

CONCLUSIONQuantitative pathologic technique combined with valid statistical methods, as an objective means of assessing prognosis, may reliably improve the outcome in lymph node negative breast cancer.

Adult ; Aged ; Breast Neoplasms ; pathology ; DNA, Neoplasm ; analysis ; Female ; Humans ; Lymphatic Metastasis ; Middle Aged ; Multivariate Analysis ; Prognosis

OBJECTIVETo clone differentially expressed cDNA sequences involved in malignant transformation induced by benzo(a)pyrene metabolite dihydroxyepoxy benzo pyrene (BPDE).

METHODThe malignant transformation of human bronchial epithelial cell line 16HBE induced by BPDE in vitro was used as a model for comparing gene expression between the transformed cells and controls. cDNA representational difference analysis (cDNA-RDA) was performed to isolate differentially expressed cDNA fragment in transformed cells. The cDNA fragments were ligated to pGEM-T vector and transformed into JM109 bacteria. The plasmid DNA were sequenced and compared with data in GenBank by BLASTN.

RESULTSFive cDNA sequences were found to be novel ones and were registered in dbest database, which assigned accession numbers in GenBank are BG354691, BG354692, BG354693, BG354694 and BG354695, respectively. Eight of the remaining cDNA sequences showed sequence homology to those previously reported such as ribosomal protein S23, MLN137, ACTN4, transforming growth factor and G protein gene.

CONCLUSIONSThese 13 genes may be involved in BPDE-induced malignant transformation, but their biological characteristics and functions are left to further studies.

Benzopyrenes ; metabolism ; pharmacology ; Carcinogens ; pharmacology ; Cell Transformation, Neoplastic ; chemically induced ; genetics ; Cells, Cultured ; Cloning, Molecular ; DNA, Complementary ; analysis ; drug effects ; DNA, Neoplasm ; analysis ; Gene Expression ; drug effects ; Humans

OBJECTIVETo investigate expression and significance of hTERT, telomerase associated-regulation protein (TRAP) and proliferating cell nuclear antigen (PCNA) in ovarian epithelial tumors.

METHODS106 specimens of ovarian epithelial tumors and their clinical history were collected, including 54 cases of malignancy, 33 borderline cases and 19 benign tumor cases. Immunohistochemical staining for hTERT, TRAP and PCNA were performed. Follow-up information was obtained for 45 of 87 cases (malignancy in 54 and borderline malignancy in 33).

RESULTSThe expression of hTERT was significantly different between benign (4/19) and borderline (90.9%, 30/33) cases, benign and malignant (94.4%, 51/54) cases (P < 0.001), as was the expression of TRAP between benign (4/15) and malignant (77.8%, 28/36) cases (P < 0.001). The expression of hTERT and TRAP was not higher in stage III, IV ovarian cancer patients than in stage I and II (P > 0.05, P > 0.3). The expression of PCNA between benign (6.9 +/- 5.9)% and borderline (26.4 +/- 17.8)% cases, benign and malignant (51.8 +/- 22.1)% cases, and borderline and malignant cases were different, and were statistically significant (P < 0.01, P < 0.001, P < 0.05). 33 cases of borderline malignancy are all survive. In 54 cases of malignancy, 35 of them have metastasis (64.8%), including 5 cases of lymph nodes metastasis. 4 of them died (7.4%).

CONCLUSIONSThe expression of hTERT and TRAP is associated with the malignant degree of ovarian cancer, but does not correlate with stage. The expression of TRAP resembles hTERT, which may be a new tumor-associated gene. Telomerase activity is positively associated with PCNA.

DNA-Binding Proteins ; Female ; Humans ; Immunohistochemistry ; Neoplasm Staging ; Ovarian Neoplasms ; enzymology ; pathology ; Proliferating Cell Nuclear Antigen ; analysis ; Telomerase ; analysis ; Transcription Factors ; analysis

OBJECTIVES: The EGFR plays an important role in tumorigenesis and tumor progression of colorectal cancer, and leads to the activation of intracellular signaling pathways. The use of anti-EGFR-targeted therapy has increased for patients with colorectal cancer, but patients with EGFR mutations will be resistant to anti-EGFR-targeted therapy. The identification of gene mutations is critical in cancer treatment; therefore, the aim of this study is to investigate the incidences of EGFR mutations in colorectal cancer patients in Korea. METHODS: We reviewed 58 colorectal cancer patients who underwent operations between 2003 and 2006, retrospectively. We analyzed their EGFR mutations in 4 loci by DNA sequencing. In addition, we analyzed the correlation between the presence of EGFR mutation and patients' clinicopathologic features. RESULTS: Of the 58 patients, 35 patients were male and 23 were female. Their mean age was 63.28+/-11.18 years. Two patients (3.45%) were diagnosed as stage Tis, 7 patients (12.07%) had stage I, 24 patients (41.38%) had stage II, 20 patients (34.48%) had stage III, and 5 patients (8.62%) had stage IV. As a result of mutational analysis, EGFR mutations on exon 20 were detected in 13 patients (22.41%, G-->A transitions). EGFR mutations on exon 18, 19 and 21 were not detected. EGFR mutation increased in the earlier stage and the absence of lymph node metastasis (P=0.028). CONCLUSION: The incidence of EGFR mutation in Korean colorectal cancer patients is 22.41%. In addition, EGFR mutation significantly increased in the earlier stage and the absence of lymph node metastasis.
Cell Transformation, Neoplastic ; Colorectal Neoplasms ; Exons ; Female ; Humans ; Incidence ; Lymph Nodes ; Male ; Neoplasm Metastasis ; Retrospective Studies ; Sequence Analysis, DNA