SUMMARY:We have delineated regions of interest at chromosome 2q21.2, 2q36.3, and 2q37.1 by deletion mapping of 114 urothelial cancers (UC). Altogether, 17%, 18%, and 63% of the G1, G2, and G3 tumors displayed loss of heterozygosity at chromosome 2q, respectively, The region at 2q21.2 was narrowed down to the LRP1B gene (NT_005129.6). Hemi-and homozygous deletion at the LRP1B gene region was seen in 31 of 114 UCs. Only 8% of the UCs with G1 and none with G2 tumors showed loss of heterozygosity at the LRP1B gene, whereas 49% of the G3 UCs had allelic loss at this region. RT-PCR analysis of the LRP1B gene showed the lack of expression of several exons in 2 of 9 cases analyzed. Our analysis suggests that the LRP1B gene is a candidate tumor suppressor gene in UCs. (Lab Invest 2002, 82:639 -643).C ancer of the urinary bladder is one of the most common tumors in the Western world. The majority of urothelial cancers (UC) are diagnosed as noninvasive tumors (Ta), whereas 20% to 25% of the cases show an invasive growth (T1-4) at the time of first presentation. From the clinical point of view, the question arises whether these two major groups of tumors are distinct entities or correspond to different stages of progression of a single tumor entity. Pioneering cytogenetic analyses before the chromosome banding era have suggested that the number of gross karyotype alterations predicts the clinical course of UCs, for example, recurrency and progression (Falor and Ward, 1978;Lamb, 1967). Later, several studies showed that allelic changes at specific chromosomal regions and alterations of tumor suppressor genes, such as PTEN, RB, and TP53, correlate with stage and grade of bladder cancers (for review see Knowles, 1999). Comparative genomic hybridization (CGH) studies also suggested quantitative differences of genetic changes, including DNA losses at chromosome 2q22-33, 2q32-qter, and 2q34-qter regions, between the noninvasive and invasive bladder cancers (Richter et al, 1997Simon et al, 1998Simon et al, , 2000. Loss of heterozygosity (LOH) at chromosome 2q is also associated with aggressive growth of head and neck and non-small cell lung carcinomas (Ransom et al, 1998;Shiseki et al, 1994). Recently, Liu et al (2000) identified a putative tumor suppressor gene LRP1B from the chromosome 2q21.2 region that was found to be homozygously deleted in several cancer cell lines, including the bladder cancer cell line VM-CUB-2. To delineate putative tumor suppressor gene regions, we analyzed 114 UCs for 20 microsatellite loci at the chromosome 2q including those from the LRP1B region. We identified three distinct regions of LOH in 40% of tumors and found a correlation between LOH at chromosome 2q and tumor grade. Results Three Target Regions of Allelic Loss at Chromosome 2qCGH analysis of 18 Grade 3 (G3) UCs of this series revealed a gain at chromosome 2p in 7 cases and loss of DNA at chromosome 2q in 11 cases (one example is shown in Fig. 2). Therefore, we evaluated score 2 at chromosome 2p as a duplication of one allele, but at chromoso...

The pathogenesis of ovarian carcinomas is heterogeneous, with even the same entities showing great variance. In our study we investigated the mutations of the BRAF, KRAS, and p53 genes in serous and mucinous borderline tumors and in low grade and high grade serous and mucinous tumors. The mutations of BRAF and KRAS genes have been shown in 60% of borderline and low grade (well differentiated) serous and mucinous tumors, but very rarely in high grade (moderately and poorly differentiated) carcinomas. However mutations of p53 are very common in high grade tumors and this indicates a "dualistic" model of ovarian tumorigenesis. A total of 80 serous tumors, including serous borderline, low grade and high grade tumors, and 23 mucinous tumors, including borderline and invasive tumors were analysed for BRAF and KRAS mutations using real time PCR method followed by melting point analysis. P53 mutation was investigated by immunohistochemistry. We assumed mutation of the p53 gene when 100% of tumor cells showed strong nuclear positivity. We observed differences in genetic alterations in the development of the low grade tumors and between low and high grade tumors too. In some bilateral or stage II-III cases we observed differences between the mutation status of the left and right ovarian tumors and between the primary tumor and its implants. In one case in a tumor with micropapillary pattern showing high grade nuclear atypia we could detect mutations in both KRAS and p53 genes. The majority of our mucinous ovarian tumor cases showed a KRAS mutation. We have not found mutations of the BRAF and p53 genes in these cases. We have found as have others, that there is a dualistic pathway of ovarian carcinogenesis. In the majority of cases, low grade epithelial tumors develop in a stepwise manner due to genetic alterations of the members of MAP-kinase pathway; however mutation of the p53 gene is the key event in the development of high grade tumors.

Urothelial cancers of the bladder (UC) comprise biologically heterogeneous group of tumors and display complex genetic alterations. Several genetic changes have been analyzed in detail and some of them are associated with the development and progression of UCs. Only a few studies, however, are focused on identifying the order in which the aberrations may appear during UC tumorigenesis. We have analyzed 123 papillary UCs of the bladder by microsatellites for each of the chromosomal regions that have been suggested to be specifically involved in this type of tumor. We used Bayesian network modeling that enables to uncover multivariate probabilistic dependencies between variables. This methodology applied to LOH data allowed us to discover patterns of losses in UCs. Exploiting the mechanism of probabilistic reasoning in Bayesian networks we suggest primary and secondary events in tumor pathogenesis and reconstruct the possible flow of progression of allelic changes. Key words: urothelial cancer; loss of heterozygosity; Bayesian networks; network inference; genetic pathwaysUrothelial carcinoma of the bladder (UC) comprise biologically and morphologically heterogenous groups of neoplasms. During the last decade a broad spectrum of genetic alterations has been described in UCs. Cytogenetic, CGH and microsatellite analyses showed loss, gain and amplification of DNA sequences at several chromosomal regions. 1 Hemi-and homozygous deletion at and methylation/mutation of the CDKN2A gene at chromosome 9p21 is considered to be an early genetic event. 2 The vast majority of UCs acquire several additional genetic alterations during progression, including deletion of chromosome 2q, 5q and 8p, deletion/ mutation of the p53 and Rb genes or amplification and overexpression of the ERBB-2 gene. [3][4][5][6][7][8] Although some of the genetic alterations occur at random, the recurrent changes may refer to a network of genes that are specifically involved in tumor development and progression.Several models indicating a step-by-step order of genetic changes as a single pathway from normal urothelial cell to malignant tumor have been proposed. [9][10][11] Desper et al. 12 and Schäffer et al. 13 applied mathematical models to infer the order of genetic changes during progression of UCs. They described the progression of alterations as a tree with a root representing the normal cell and used 2 different tree models. In a distance-based tree leaf nodes represent genetic aberrations. The distance function between the nodes in the tree was defined based on probabilities of the co-occurrence of genetic events. A distance-based phylogenetic tree-building algorithm was used to infer the tree structure that fits the pairwise distances at best. Alternatively, a maximum weight branching algorithm was used to reconstruct a tree in which both internal nodes and leaf nodes correspond to aberrations. A major limitation of these models is that they describe the progression of genetic events as trees, whereas the biological intuition suggests that this...

Objectives: Many cellular functions are controlled by cell-cell and cell-matrix interactions. It has recently been found that syndecans, transmembrane heparan sulphate (HS) proteoglycans, can act as receptors or co-receptors and modulate cell adhesion. Our aim was to study the role of syndecan-1 in the aggregation of human lymphoma cells, and to investigate its effect on cell survival. Methods: Immunocytochemistry, confocal laser scanning microscopy, flow cytometry and aggregation/reaggregation bio-assays were used on HT58, BL41/95 and Raji lymphoma cell lines. Results: Bio-assays showed that the aggregation of HT58 cells was inhibited by heparin, HS, removal of the HS chain and binding of the anti-syndecan-1 monoclonal antibody. In the search for a counter-receptor of syndecan-1, several adhesion molecules were tested, but none of them proved to be the adhesion partner. In the case of heparitinase/trypsin digestion with long-term inhibition of HS synthesis (sodium chlorate treatment), the inhibited aggregation was accompanied by cell cycle arrest and the induction of apoptosis. Conclusions: The results obtained showed that surface syndecan-1 expression contributes to homotypic adhesion. In addition, HS chains, including those on syndecan-1, take part in the regulation of cell proliferation and active cell death in HT58 lymphoma cells.

In the diagnostic workflow we need to think in algorithms, containing more assays. One of the most important task in the management of cancer patient is to detect nucleic acid sequence changes in clinical specimens. Before using the most expensive method to analyze direct our targets, a screening assay is needed to reduce the number of samples. In the detection of gene-sequence alterations classical screening methods are available, as SSCP, DGGE or TGGE, (Finke Exp Clin Endocrinol Diabetes 104:92-97, 1996; Lessa and Applebaum Mol Ecol 2:119-129, 1993) however these are very time consuming processes. At this time in the molecular lab the real-time PCR equipments are very popular and with the function of melting curve analysis it can be a very convenient, simple and cost-efficient screening method.

THE JOURNAL OF UROLOGY® treated with 2 doses of 200 ug/ml of the antisense vector each 2 days apart were reduced by 75% by the antisense CK2-alpha compared to tumors treated with the control vector. Substantial apoptosis (>80%) was noted in the in vitro and in vivo 253J-BV cells treated with antisense CK2-alpha but not iin those treated with the control vector.CONCLUSIONS: Treatment with an antisense CK2-alpha construct decreases CK2 expression and activity and induces regression in human bladder cancer cells. These results demonstrate the potential for antisense CK2 therapy as a novel therapeutic strategy for bladder cancer.

During diagnostic workflow when detecting sequence alterations, sometimes it is important to design an algorithm that includes screening and direct tests in combination. Normally the use of direct test, which is mainly sequencing, is limited. There is an increased need for effective screening tests, with "closed tube" during the whole process and therefore decreasing the risk of PCR product contamination. The aim of this study was to design such a closed tube, detection probe based screening assay to detect different kind of sequence alterations in the exon 11 of the human c-kit gene region. Inside this region there are variable possible deletions and single nucleotide changes. During assay setup, more probe chemistry formats were screened and tested. After some optimization steps the taqman probe format was selected.