Prostate cancer and the genomic revolution: Advances using microarray analyses

Lycopene modulates growth and survival associated genes in prostate cancer

Lycopene is a fat soluble red-orange carotenoid pigment present in tomato that reduces the risk for prostate cancer, a common malignancy among men. However, the mechanism by which lycopene attenuates prostate cancer is not fully defined. In this study we examined the effect of lycopene on proliferation, survival, and biomarker gene expression in prostate cancer (PC-3) cells in culture. WST-1 assay showed that lycopene induces a biphasic effect on PC-3 cells with a modest increase in proliferation at 1-5 μM, no change at 10-25 μM and a decrease at 50-100 μM doses in culture. Interestingly, combination treatment with lycopene induced anti-proliferative effect of Temozolomide on PC-3 cells. Lycopene also augmented the anti-proliferative effect of peroxisome proliferator-activated receptor gamma (PPARγ) agonists, but not Doxorubicin or Taxol, in prostate cancer. Flow cytometry analyses showed that lycopene, in combination with chemotherapeutic agents and PPARγ agonists, induced modest cell cycle arrest with significant increase in cell death by apoptosis and necrosis on prostate cancer. Gene array and quantitative reverse transcription polymerase chain reaction analyses showed that lycopene alters the expression of growth and apoptosis associated biomarkers in PC-3 cells. These findings highlight that lycopene attenuates prostate cancer by modulating the expression of growth and survival associated genes.

Isoflavones and the prevention of breast and prostate cancer: new perspectives opened by nutrigenomics

Epidemiological evidence together with preclinical data from animal and in vitro studies strongly support a correlation between soy isoflavone consumption and protection towards breast and prostate cancers. The biological processes modulated by isoflavones, and especially by genistein, have been extensively studied, yet without leading to a clear understanding of the cellular and molecular mechanisms of action involved. This review discusses the existing gaps in our knowledge and evaluates the potential of the new nutrigenomic approaches to improve the study of the molecular effects of isoflavones. Several issues need to be taken into account for the proper interpretation of the results already published for isoflavones. Too often knowledge on isoflavone bioavailability is not taken into account; supra-physiological doses are frequently used. Characterization of the individual variability as defined by the gut microflora composition and gene polymorphisms may also help to explain the discrepancies observed so far in the clinical studies. Finally, the complex inter-relations existing between tissues and cell types as well as cross-talks between metabolic and signalling pathways have been insufficiently considered. By appraising critically the abundant literature with these considerations in mind, the mechanisms of action that are the more likely to play a role in the preventive effects of isoflavones towards breast and prostate cancers are reviewed. Furthermore, the new perspectives opened by the use of genetic, transcriptomic, proteomic and metabolomic approaches are highlighted.

Overexpression of CD24, c-myc and phospholipase 2A in prostate cancer tissue samples obtained by needle biopsy

Altered CD24, c-myc and phospholipase 2a expression was reported in different cancers. Our aim was to measure the expression of these genes in prostate cancer tissues, and compare it to non-cancerous samples. Prostate tissue samples were collected by needle biopsy from 20 prostate cancer (PCA) and 11 benign prostate hyperplasic (BPH) patients. RNA was isolated; cDNA synthetized, CD24, c-myc and phospholipase 2A (PL2A) expressions were determined by quantitative real-time PCR method. The expression of beta-globin gene was measured for normalization of the gene expression results. Serum prostate specific antigen (PSA) levels were determined by microparticle enzyme immunoassay (MEIA) method. PSA levels were significantly different between the PCA and BPH groups, 252.37 +/- 308.33 ng/ml vs. 3.5 +/- 2.14 ng/ml (p = 0.001), respectively. CD24 expression was 988.86 +/- 3041 ng/microl in prostate tumor and 4.00 +/- 4.25 ng/microl in the BPH group (p = 0.035). The c-myc expression was 88.32 +/- 11.93 ng/microl in the prostate tumor and 17.08 +/- 21.75 ng/microl in the BPH group (p = 0.02), and the PL2A 31.36 +/- 67.02 ng/microl was in PCA and 5.56 +/- 14.08 ng/microl in BPH (p = 0.025). Gleason's scores showed correlation with c-myc (p = 0.019) and PSA (p = 0.033) levels. Overexpression of PL2A, CD24 and c-myc was observed in prostate cancer samples using quantitative real-time PCR method.

Gene expression assays

The study of the profile of gene expression in a cell or tissue at a particular moment gives an insight into the plans of the cell for protein synthesis. Recent technological advances make it possible to analyze the expression of the entire genome in a single experiment. These "gene expression assays" complement or replace previous assays which measured the gene expression of only one gene, or a select group of genes. Within this chapter we outline the development of the gene expression assay and provide examples of the wide range of disciplines in which it is used. An overview of the current technologies is given, and includes an introduction to laser capture microdissection and linear amplification of RNA, both of which have extended the application of gene expression assays. Illustrative examples in the field of cancer and neuroscience highlight the scientific achievements. This technology has made in understanding the pathogenesis of diseases, including breast cancer, Huntington's disease, and schizophrenia. With recent advances including exon arrays to investigate alternative splicing, tiling arrays to investigate novel transcription start sites, and on-chip chromatin immunoprecipitation to investigate DNA-protein interactions, the future of gene expression assays is set to further our understanding of the complexities of gene expression.

mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer

Background

Colorectal cancer develops through two main genetic instability pathways characterized by distinct pathologic features and clinical outcome.

Results

We investigated colon cancer samples (23 characterized by microsatellite stability, MSS, and 16 by high microsatellite instability, MSI-H) for genome-wide expression of microRNA (miRNA) and mRNA. Based on combined miRNA and mRNA gene expression, a molecular signature consisting of twenty seven differentially expressed genes, inclusive of 8 miRNAs, could correctly distinguish MSI-H versus MSS colon cancer samples. Among the differentially expressed miRNAs, various members of the oncogenic miR-17-92 family were significantly up-regulated in MSS cancers. The majority of protein coding genes were also up-regulated in MSS cancers. Their functional classification revealed that they were most frequently associated with cell cycle, DNA replication, recombination, repair, gastrointestinal disease and immune response.

Conclusion

This is the first report that indicates the existence of differences in miRNA expression between MSS versus MSI-H colorectal cancers. In addition, the work suggests that the combination of mRNA/miRNA expression signatures may represent a general approach for improving bio-molecular classification of human cancer.

Application of Genomic Technologies to Human Prostate Cancer

Prostate cancer is the most commonly diagnosed non-cutaneous malignancy in U.S. males and has a broad spectrum of clinical behavior ranging from indolent to lethal. Microarray technology has provided unprecedented opportunity to explore the genetic processes underlying prostate cancer by providing a comprehensive survey of a cell's transcriptional landscape. Prostate cancer, however, has posed significant challenges that have contributed to inconsistent results between studies and difficulty replicating findings. Despite these challenges, several important insights have been gained along with new clinical biomarkers of diagnosis and prognosis. Continued improvements in methods of tissue preparation, microarray technology and data analysis will overcome existing challenges and fuel future discoveries.

Quantitative real-time RT-PCR of CD24 mRNA in the detection of prostate cancer

Background

Gene expression profiling has recently shown that the mRNA for CD24 is overexpressed in prostate carcinomas (Pca) compared to benign or normal prostate epithelial tissues. Immunohistochemical studies have reported the usefulness of anti-CD24 for detecting prostate cancer over the full range of prostate specimens encountered in surgical pathology, e.g. needle biopsies, transurethral resection of prostate chips, or prostatectomies. It is a small mucin-like cell surface protein and thus promises to become at least a standard adjunctive stain for atypical prostate biopsies. We tested the usefulness of real-time RT-PCR for specific and sensitive detection of CD24 transcripts as a supplementary measure for discriminating between malignant and benign lesions in prostatic tissues.

Methods

Total RNA was isolated from snap-frozen chips in 55 cases of benign prostatic hyperplasia (BPH) and from frozen sections in 59 prostatectomy cases. The latter contain at least 50% malignant epithelia. Relative quantification of CD24 transcripts was performed on the LightCycler instrument using hybridization probes for detection and porphobilinogen deaminase transcripts (PBGD) for normalization.

Results

Normalized CD24 transcript levels showed an average 2.69-fold increase in 59 Pca-cases (mean 0.21) when compared to 55 cases of BPH (mean 0.08). This difference was highly significant (p < 0.0001). The method has a moderate specificity (47.3%) but a high sensitivity (86.4%) if the cutoff is set at 0.0498. CD24 expression levels among Pca cases were not statistically associated with the tumor and lymph-node stage, the grading (WHO), the surgical margins, or the Gleason score.

Conclusion

The present study demonstrates the feasibility of quantitative CD24 RNA transcript detection in prostatic tissues even without previous laser microdissection.

Tissue print micropeel: a new technique for mapping tumor invasion in prostate cancer

Because of widely adopted screening programs for early detection of prostate cancers, many patients who undergo radical prostatectomy have tumors that are not grossly evident, and the extent and distribution of the cancer in the gland can only be determined by a microscopic examination of the surgical specimen. Historically, one of the most important predictors of the quality of cancer control following surgical resection of a solid tumor is the absence of cancer at the surgical margins. Although the clinical significance of cancer at the margins of a radical prostatectomy specimen has been a source of controversy in recent years, surgical pathology assessment of radical prostatectomy margins remains an important part of prostate cancer clinical care. However, a comprehensive histopathologic review of every radical prostatectomy specimen is beyond the resources of most hospitals. Tissue print micropeel technologies, combined with appropriate markers, provide a new strategy that combines a relatively simple technique for sampling specimen margins with a method for obtaining molecular information about the cancer that can add to the macroscopic and microscopic anatomical findings. This new tissue printing approach for incorporating molecular markers into the assessment of radical prostatectomy margins is reviewed in this article.

Mode of growth determines differential expression of prostasomes in cultures of prostate cancer cell lines and opens for studies of prostasome gene expression

The exocrine secretion of the acinar gland cells in the human prostate consists of, among other components, a serous secretion and prostasomes. The prostasomes are functionally associated with both reproduction and prostate cancer development and are capable to raise autoantibodies at various pathologies. Therefore, we are trying to characterize prostasome antigens by analysing prostasome-producing cell lines of prostate cancers with the cDNA microarray technique. To obtain one state with synthesis of prostasomes and another state without synthesis, we checked whether the prostasome differentiation was influenced by the mode of growing the cells, that is, whether the cells had been growing on a solid support or on a flexible one. We studied the expression of prostasomes in the cell lines PC3, DU145 and LNCaP. We grew the cells with the following methods: Monocellular layers on microbeads, multicellular spheroids, single cells in suspension cultures, and xenotransplants in nude rats. The presence of prostasomes was examined by ELISA, immunocytochemistry or electron microscopy. The results showed that growing the cells on microbeads (solid support) produced a differentiation of prostasomes, while growing the cells in multicellular spheroids (flexible support) did not. Thus it should be possible to apply cDNAmicroarray analyses for characterizing the genes which are active at the cellular expression of prostasomes and then deduce the prostasome antigens.

Genomics of prostate cancer: Is there anything to „translate”?

This review provides an up-dated collection of data concerning the genetic and epigenetic changes during development, growth and progression of prostate cancer. Hereditary and susceptibility factors have a long list, similarly to the expression of single genes connected to various cell functions. It was a hope that covering a large set of genes, array technologies would clarify very rapidly the role of genetics in malignant diseases, offering targets for molecular diagnostics and therapy. The power of high-throughput techniques for the detection and global analysis of gene expression is unquestionable, interesting, astonishing as well as puzzling data have already been obtained. However, the standardization of the procedures is still missing and the reproducibility is rather low in many instances. Moreover, the different array methods can select different gene expression profiles, which makes the decision rather difficult. Another important question is, coming again from the array technologies, how far the genotype (the gene profiles or fingerprints) can reflect the actual phenotype in a highly complex and readily changing disease as cancer. Proteomics will provide a closer look to this seemingly unanswerable problem. We are at the beginning of the exploration of the behavior of cancer cells in order to apply a more effective therapy based on a more reliable set of diagnostic and prognostic informations.