DNA microarrays in prostate cancer

A modern era of personalized medicine in the diagnosis, prognosis, and treatment of prostate cancer

The present era is witnessing rapid advancements in the field of medical informatics and modern healthcare management. The role of translational bioinformatics (TBI), an infant discipline in the field of medical informatics, is pivotal in this revolution. The development of high-throughput technologies [e.g., microarrays, next-generation sequencing (NGS)] has propelled TBI to the next stage in this modern era of medical informatics. In this review, we assess the promising translational outcomes of microarray- and NGS-based discovery of genes, proteins, micro RNAs, and other active biological compounds aiding in the diagnosis, prognosis, and therapy of prostate cancer (PCa) to improve treatment strategies at the localized and/or metastatic stages in patients. Several promising candidate biomarkers in circulating blood (miR-25-3p and miR-18b-5p), urine (miR-95, miR-21, miR-19a, and miR-19b), and prostatic secretions (miR-203) have been identified. AURKA and MYCN, novel candidate biomarkers, were found to be specifically expressed in neuroendocrine PCa. The use of BTNL2 gene mutations and inflammasomes as biomarkers in immune function-mediated, inherited PCa has also been elucidated based on NGS data. Although TBI discoveries can benefit clinical performance metrics, the translational potential and the in vivo performance of TBI outcomes need to be verified. In conclusion, TBI aids in the effective clinical management of PCa; furthermore, the fate of personalized/precision medicine mostly relies on the enhanced diagnostic, prognostic, and therapeutic potential of TBI.

Prostate cancer and the genomic revolution: Advances using microarray analyses

The emerging technology of microarray analysis allows the establishment of molecular portraits of prostate cancer and the discovery of novel genes involved in the carcinogenesis process. Many novel genes have already been identified using this technique, and functional analyses of these genes are currently being tested. The combination of microarray analysis with other recently developed high-throughput techniques, such as proteomics, tissue arrays, and gene promoter-methylation, especially using tissue microdissection methods, will provide us with more comprehensive insights into how prostate cancer develops and responds to gene-targeted therapies. Animal models of prostate cancer are being characterized by high throughput techniques to better define the similarities and differences between those models and the human disease, and to determine whether particular models may be useful for specific targeted therapies in pre-clinical studies. Although profiling of mRNA expression provides important information of gene expression, the development of proteomic technologies will allow for an even more precise global insight into cellular signaling and structural alterations during prostate carcinogenesis. Not only will the "omic" revolution change basic science, but it will lead to a new era of molecular medicine.

Molecular aspects of prostate cancer: implications for future directions

Many studies have been developed trying to understand the complex molecular mechanisms involved in oncogenesis and progression of prostate cancer (PCa). Current biotechnological methodologies, especially genomic studies, are adding important aspects to this area. The construction of extensive DNA sequence data and gene expression profiles have been intensively explored to search for candidate biomarkers to evaluate PCa. The use of DNA micro-array robotic systems constitutes a powerful approach to simultaneously monitor the expression of a great number of genes. The resulting gene expressing profiles can be used to specifically describe tumor staging and response to cancer therapies. Also, it is possible to follow PCa pathological properties and to identify genes that anticipate the behavior of clinical disease. The molecular pathogenesis of PCa involves many contributing factors, such as alterations in signal transduction pathways, angiogenesis, adhesion molecules expression and cell cycle control. Also, molecular studies are making clear that many genes, scattered through several different chromosomal regions probably cause predisposition to PCa. The discovery of new molecular markers for PCa is another relevant advance resulting from molecular biology studies of prostate tumors. Interesting tissue and serum markers have been reported, resulting in many cases in useful novelties to diagnostic and prognostic approaches to follow-up PCa. Finally, gene therapy comes as an important approach for therapeutic intervention in PCa. Clinical trials for PCa have been demonstrating that gene therapy is relatively safe and well tolerated, although some improvements are yet to be developed.

Novel molecular aspects of prostate carcinogenesis

Prostate adenocarcinoma is one of the most frequently diagnosed forms of cancer in the male population of the Western world. The pivotal role of androgen and its receptor in this disease has been abundantly documented and indeed, chemical castration and treatment with antiandrogens are now standard therapies. However, relapse is often observed after 18-24 months, due to the remarkable ability of prostate tumour cells to adapt to low or undetectable androgen levels. Amplification and mutations of the androgen receptor (AR) gene have been described as well as alterations in cofactor expression and crosstalk with other signalling pathways. Another recent line of research focused on the re-programming of gene expression taking place in prostate tumours. Global expression profiling of normal and cancerous prostate tissues led to the identification of tumour-distinctive patterns. Validation studies are currently underway to identify novel drug targets as well as diagnostic and outcome prediction markers.

In silico dissection of cell-type-associated patterns of gene expression in prostate cancer

Prostate tumors are complex entities composed of malignant cells mixed and interacting with nonmalignant cells. However, molecular analyses by standard gene expression profiling are limited because spatial information and nontumor cell types are lost in sample preparation. We scored 88 prostate specimens for relative content of tumor, benign hyperplastic epithelium, stroma, and dilated cystic glands. The proportions of these cell types were then linked in silico to gene expression levels determined by microarray analysis, revealing unique cell-specific profiles. Gene expression differences for malignant and nonmalignant epithelial cells (tumor versus benign hyperplastic epithelium) could be identified without being confounded by contributions from stroma that dominate many samples or sacrificing possible paracrine influences. Cell-specific expression of selected genes was validated by immunohistochemistry and quantitative PCR. The results provide patterns of gene expression for these three lineages with relevance to pathogenetic, diagnostic, and therapeutic considerations.

Age-associated changes in histology and gene-expression profile in the rat ventral prostate

The incidence of prostate diseases rises dramatically with age in men, yet little is understood of the mechanisms underlying prostatic senescence and its contribution to disease development in the gland. In Noble rats, aging of the ventral prostate (VP) is characterized morphologically by widespread atrophy of acini, increased accumulation of concretions in glandular lumen, infiltration of inflammatory cells, and focal epithelial atypia. We used a cDNA microarray containing 2388 known transcripts, together with the Tyramide Amplification System and t statistics, to identify differentially expressed genes in the VPs of young (3 months old) and old (16 months old) rats. A total of 78 VP genes were found to be differentially expressed by the two groups; in old rats, 65 VP genes (83%) showed reduced expression and 13 genes (17%) showed increased expression compared with young animals. The age-dependent underexpressed genes fell into several functional clusters: those involved in amino-acid metabolism, protein synthesis, protein secretion and degradation, vesicle/membrane trafficking, energy metabolism, signal transduction, spermidine and spermine syntheses, and cellular defense against stress. The overexpressed genes included iduronate 2-sulfatase, HLA class I locus C heavy chain, membrane cofactor protein of the complement system, TRPM-2, cadherin-associated protein-related, and X-CGD. Post hoc analyses confirmed a progressive decline in the expression of ribophorin II and BiP and a gradual increase in the expression of TRPM-2 in rat VPs as animals aged from 3 to 19 months old. In conclusion, the observed widespread declines in expression of genes involved in protein synthesis, protein fidelity maintenance, anabolism, growth inhibition, and energy metabolism, together with increased expression of genes implicated in cell survival in the VPs of senescent rats, may help explain the susceptibility of the prostates of elderly men to development of disease.