Laser-captured microdissection-microarray analysis of the genes involved in endometrial carcinogenesis: stepwise up-regulation of lipocalin2 expression in normal and neoplastic endometria and its functional relevance

Endometrial carcinoma often arises from normal endometrial glandular cells via a precursor, atypical endometrial hyperplasia. However, the genetic changes involved in this carcinogenetic process are not fully understood. Differentially expressed genes were selected from glandular cells of normal proliferative-phase endometria, atypical endometrial hyperplasia, and endometrial carcinoma using laser-captured microdissection and microarray. The microarray analysis revealed a total of 51 genes to be up-regulated and 23 genes to be down-regulated in neoplastic endometrial epithelia. We focused on lipocalin2 (LCN2), which showed the largest magnitude of up-regulation. Immunostaining for lipocalin2 confirmed a stepwise increase in its expression in endometrial hyperplasia and carcinoma. In addition, elevated expression of lipocalin2 was correlated with the poor outcome of endometrial carcinoma patients. The subcellular distribution of lipocalin2 was both cytoplasmic and nuclear, despite reports that lipocalin2 is a secretory protein. Treatment of endometrial carcinoma cells with 5-azacytidine increased the expression of lipocalin2, suggesting the expression to be controlled by methylation of the promoter. The forced expression of lipocalin2 resulted in the enhanced cell proliferation and invasion in vitro. The expression of lipocalin2 increased with the endometrial carcinogenesis, and accumulation of the protein conferred biological aggressiveness to endometrial carcinoma cells. These results suggest lipocalin2 to be a novel target in the treatment of endometrial carcinoma.ArticleHUMAN PATHOLOGY. 42(9):1265-1274 (2011)journal articl

A flexible representation of omic knowledge for thorough analysis of microarray data

BACKGROUND: In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e.g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML) that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. RESULTS: In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi) by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. As a result, we have discovered a new insight that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress. In addition to this novel discovery, similar findings previously reported were also quickly confirmed using GSCope3 and BiKLi. CONCLUSION: GSCope3 can statistically analyze microarray data in the context of any OSML-represented omic knowledge. OSML is not restricted to a specific data type structure, but it can represent a wide range of omic knowledge. It allows us to convert new types of omic knowledge into datasets that can be used for microarray data analysis with GSCope3. In addition to BiKLi, by collecting various types of omic knowledge as OSML libraries, it becomes possible for us to conduct detailed thorough analysis from various biological viewpoints. GSCope3 and BiKLi are available for academic users at our web site

cDNA cloning of a human brain finger protein, BFP/ZNF179, a member of the RING finger protein family.

The rat bfp/znf179 transcript for a member of the RING finger protein family, is expressed in brain and up-regulated in neural differentiation of P19 embryonic carcinoma cells. Here we report the full-length cDNA structure of human BFP/ZNF179 and its expression profile. The cDNA clone consists of 3082 nucleotides and encodes an open reading frame of a 632-amino acid protein that contains a RING finger domain at its N-terminus, and alanine-rich and glycine-rich domains at its C-terminus. Reverse transcriptase polymerase chain reaction analysis of various human tissues indicated that BFP/ZNF179 is predominantly expressed in brain

Induction of a BrdU-enhanceable fragile site-like lesion and sister chromatid exchanges at 11q23.1 in EBV-transformed lymphoblastoid cell lines.

We examined the expression of a fragile site-like lesion and induction of sister chromatid exchanges (SCEs) at 11q23.1 in EBV-transformed lymphoblastoid cell lines derived from carriers of distamycin A-inducible fragile sites and ataxia telangiectasia patients. The fragile site-like lesion at 11q23.1 was found to be BrdU-enhanceable in all cell lines examined, and the expression frequencies increased linearly with the rates of BrdU substitution in replicated DNA. In addition, an increased frequency of SCEs was observed at 11q23.1 on the expressed chromosome. Thus, the BrdU-enhanceable fragile site-like lesion at 11q23.1 is a "hot spot" for the formation of SCEs, as has been reported for other rare and common fragile sites