Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle

Correlation analysis between immune-related genes and cell infiltration revealed prostate cancer immunotherapy biomarkers linked to T cells gamma delta

Prostate cancer (PCa) is a urological malignancy with poor prognosis. Immune-related genes are associated with immune infiltration in prostate cancer, but their role in immunogenic PCa is less well understood. We assessed the infiltration patterns of 22 immune cells in PCa and the relationship of immune-related differentially expressed genes (IDEGs) with them. The 87 IDEGs are involved in the interaction between the extracellular matrix and the tumor microenvironment. The model, including seven IDEGs (SLPI, DES, IAPP, NPY, ISG15, PLA2G2A, and HLA-DMB), showed a good predictive power. The SLPI expression is positively correlated with the infiltration level of T cells gamma delta. In addition, PCa has high infiltration levels in Macrophages M1 (18.07%) and Dendritic cells activated (17.64%). The correlation analysis between IDEGs and immune cell infiltration suggested that PCa immunotherapy biomarkers may be closely related to T cells gamma delta.

Identification of a distinct luminal subgroup diagnosing and stratifying early stage prostate cancer by tissue-based single-cell RNA sequencing

BACKGROUND

The highly intra-tumoral heterogeneity and complex cell origination of prostate cancer greatly limits the utility of traditional bulk RNA sequencing in finding better biomarker for disease diagnosis and stratification. Tissue specimens based single-cell RNA sequencing holds great promise for identification of novel biomarkers. However, this technique has yet been used in the study of prostate cancer heterogeneity.

METHODS

Cell types and the corresponding marker genes were identified by single-cell RNA sequencing. Malignant states of different clusters were evaluated by copy number variation analysis and differentially expressed genes of pseudo-bulks sequencing. Diagnosis and stratification of prostate cancer was estimated by receiver operating characteristic curves of marker genes. Expression characteristics of marker genes were verified by immunostaining.

RESULTS

Fifteen cell groups including three luminal clusters with different expression profiles were identified in prostate cancer tissues. The luminal cluster with the highest copy number variation level and marker genes enriched in prostate cancer-related metabolic processes was considered the malignant cluster. This cluster contained a distinct subgroup with high expression level of prostate cancer biomarkers and a strong distinguishing ability of normal and cancerous prostates across different pathology grading. In addition, we identified another marker gene, Hepsin (HPN), with a 0.930 area under the curve score distinguishing normal tissue from prostate cancer lesion. This finding was further validated by immunostaining of HPN in prostate cancer tissue array.

CONCLUSION

Our findings provide a valuable resource for interpreting tumor heterogeneity in prostate cancer, and a novel candidate marker for prostate cancer management.

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.

Cellular Retinoic-Acid Binding Protein 2 in Solid Tumor

The retinoic acid (RA) signaling pathway is crucial for many biological processes. The RA transporter, Cellular Retinoic-Acid Binding Protein 2 (CRABP2), is abnormally expressed in various tumor types. CRABP2 presents significant effects on tumorous behaviors and functions, including cell proliferation, apoptosis, invasion, migration, metastasis, and angiogenesis. The tumorigenesis mechanism of CRABP2, as both suppressor and promotor, is complicated, therefore, there remains the need for further investigation. Elucidating the regulating mechanisms in a specific stage of the tumor could facilitate CRABP2 to be a biomarker in cancer diagnosis and prognosis. Besides, clarifying the pathways of CRABP2 in cancer development will contribute to the gene-targeted therapy. In this review, we summarized the expression, distribution, and mechanism of CRABP2 in solid tumors. Illuminating the CRABP2 signaling pathway may benefit understanding the retinoid signaling pathway, providing a useful biomarker for future clinical trials.

Trends in Gene Expression Profiling for Prostate Cancer Risk Assessment: A Systematic Review

OBJECTIVES

The aim of the study is to review biotechnology advances in gene expression profiling on prostate cancer (PCa), focusing on experimental platform development and gene discovery, in relation to different study designs and outcomes in order to understand how they can be exploited to improve PCa diagnosis and clinical management.

METHODS

We conducted a systematic literature review on gene expression profiling studies through PubMed/MEDLINE and Web of Science between 2000 and 2016. Tissue biopsy and clinical gene profiling studies with different outcomes (e.g., recurrence, survival) were included.

RESULTS

Over 3,000 papers were screened and 137 full-text articles were selected. In terms of technology used, microarray is still the most popular technique, increasing from 50 to 70% between 2010 and 2015, but there has been a rise in the number of studies using RNA sequencing (13% in 2015). Sample sizes have increased, as well as the number of genes that can be screened all at once, but we have also observed more focused targeting in more recent studies. Qualitative analysis on the specific genes found associated with PCa risk or clinical outcomes revealed a large variety of gene candidates, with a few consistent cross-studies.

CONCLUSIONS

The last 15 years of research in gene expression in PCa have brought a large volume of data and information that has been decoded only in part, but advancements in high-throughput sequencing technology are increasing the amount of data that can be generated. The variety of findings warrants the execution of both validation studies and meta-analyses. Genetic biomarkers have tremendous potential for early diagnosis of PCa and, if coupled with other diagnostics (e.g., imaging), can effectively be used to concretize less-invasive, personalized prediction of PCa risk and progression.

Cellular retinoid binding-proteins, CRBP, CRABP, FABP5: Effects on retinoid metabolism, function and related diseases

Cellular binding-proteins (BP), including CRBP1, CRBP2, CRABP1, CRABP2, and FABP5, shepherd the poorly aqueous soluble retinoids during uptake, metabolism and function. Holo-BP promote efficient use of retinol, a scarce but essential nutrient throughout evolution, by sheltering it and its major metabolite all-trans-retinoic acid from adventitious interactions with the cellular milieu, and by imposing specificity of delivery to enzymes, nuclear receptors and other partners. Apo-BP reflect cellular retinoid status and modify activities of retinoid metabolon enzymes, or exert non-canonical actions. High ligand binding affinities and the nature of ligand sequestration necessitate external factors to prompt retinoid release from holo-BP. One or more of cross-linking, kinetics, and colocalization have identified these factors as RDH, RALDH, CYP26, LRAT, RAR and PPARβ/δ. Michaelis-Menten and other kinetic approaches verify that BP channel retinoids to select enzymes and receptors by protein-protein interactions. Function of the BP and enzymes that constitute the retinoid metabolon depends in part on retinoid exchanges unique to specific pairings. The complexity of these exchanges configure retinol metabolism to meet the diverse functions of all-trans-retinoic acid and its ability to foster contrary outcomes in different cell types, such as inducing apoptosis, differentiation or proliferation. Altered BP expression affects retinoid function, for example, by impairing pancreas development resulting in abnormal glucose and energy metabolism, promoting predisposition to breast cancer, and fostering more severe outcomes in prostate cancer, ovarian adenocarcinoma, and glioblastoma. Yet, the extent of BP interactions with retinoid metabolon enzymes and their impact on retinoid physiology remains incompletely understood.

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation

The NKX3.1 homeobox gene plays essential roles in prostate differentiation and prostate cancer. We show that loss of function of Nkx3.1 in mouse prostate results in down-regulation of genes that are essential for prostate differentiation, as well as up-regulation of genes that are not normally expressed in prostate. Conversely, gain of function of Nkx3.1 in an otherwise fully differentiated nonprostatic mouse epithelium (seminal vesicle) is sufficient for respecification to prostate in renal grafts in vivo. In human prostate cells, these activities require the interaction of NKX3.1 with the G9a histone methyltransferase via the homeodomain and are mediated by activation of target genes such as UTY (KDM6c), the male-specific paralog of UTX (KDM6a) We propose that an NKX3.1-G9a-UTY transcriptional regulatory network is essential for prostate differentiation, and we speculate that disruption of such a network predisposes to prostate cancer.

Notch promotes tumor metastasis in a prostate-specific Pten-null mouse model

Although Notch signaling is deregulated in prostate cancer, the role of this pathway in disease development and progression is not fully understood. Here, we analyzed 2 human prostate cancer data sets and found that higher Notch signaling correlates with increased metastatic potential and worse disease survival rates. We used the Pten-null mouse prostate cancer model to investigate the function of Notch signaling in the initiation and progression of prostate cancer. Disruption of the transcription factor RBPJ in Pten-null mice revealed that endogenous canonical Notch signaling is not required for disease initiation and progression. However, augmentation of Notch activity in this model promoted both proliferation and apoptosis of prostate epithelial cells, which collectively reduced the primary tumor burden. The increase in cellular apoptosis was linked to DNA damage-induced p53 activation. Despite a reduced primary tumor burden, Notch activation in Pten-null mice promoted epithelial-mesenchymal transition and FOXC2-dependent tumor metastases but did not confer resistance to androgen deprivation. Notch activation also resulted in transformation of seminal vesicle epithelial cells in Pten-null mice. Our study highlights a multifaceted role for Notch signaling in distinct aspects of prostate cancer biology and supports Notch as a potential therapeutic target for metastatic prostate cancer.

ProSim: A Method for Prioritizing Disease Genes Based on Protein Proximity and Disease Similarity

Predicting disease genes for a particular genetic disease is very challenging in bioinformatics. Based on current research studies, this challenge can be tackled via network-based approaches. Furthermore, it has been highlighted that it is necessary to consider disease similarity along with the protein's proximity to disease genes in a protein-protein interaction (PPI) network in order to improve the accuracy of disease gene prioritization. In this study we propose a new algorithm called proximity disease similarity algorithm (ProSim), which takes both of the aforementioned properties into consideration, to prioritize disease genes. To illustrate the proposed algorithm, we have conducted six case studies, namely, prostate cancer, Alzheimer's disease, diabetes mellitus type 2, breast cancer, colorectal cancer, and lung cancer. We employed leave-one-out cross validation, mean enrichment, tenfold cross validation, and ROC curves to evaluate our proposed method and other existing methods. The results show that our proposed method outperforms existing methods such as PRINCE, RWR, and DADA.

Proteomic analysis reveals a proteolytic feedback loop in murine seminal fluid

BACKGROUND

Matrix metalloproteinase 9 (MMP9) has been implicated in extracellular matrix (ECM) remodelling, angiogenesis and inflammation. However, the targets for proteolysis that lead to these physiological consequences are often undefined as is the regulation of MMP9 itself. Therefore, identification of both the potential direct and indirect targets of MMP9 is critical for further understanding the effects of its proteolytic cascades.

METHODS

To study these cascades on a wider scale, transgenic mouse "knock-out" models and ultra-high performance liquid chromatography mass spectroscopy (UPLC-MS(E) ) were used to elucidate the MMP9 targets, inhibitors, and interactors found in mouse seminal vesicle fluid (SVF).

RESULTS

Proteomics analysis of SVF from wild type, mmp9-/- or pn1-/- mice detected differences in serine protease inhibitors (serpins), reproductive proteins, developmental regulators, and cancer proto-oncogenes, including Renin 1/2. Protease nexin 1 (PN1), an ECM-based inhibitor of urokinase, was elevated in the SVF of mmp9-/- mice. We observed that MMP9-mediated N-terminal cleavage of PN1 reduces this serpin's functional activity. Our data also suggest a feedback loop in which inhibition of PN1 is a critical step in permitting greater activity of MMP9.

CONCLUSION

This study extends the degradome of MMP9 and examines components relevant to seminal fluid physiology. PN1 is proposed to be a novel inhibitor of MMP9 activity and a block to collagen cleavage, a frequent antecedent to cancer cell invasion. The interaction of MMP9 with PN1 and other serpins may lead to a better understanding of seminal vesicle function and possible impacts on fertility, as well as provide novel therapeutic targets.

Differentially expressed androgen-regulated genes in androgen-sensitive tissues reveal potential biomarkers of early prostate cancer

Background

Several data favor androgen receptor implication in prostate cancer initiation through the induction of several gene activation programs. The aim of the study is to identify potential biomarkers for early diagnosis of prostate cancer (PCa) among androgen-regulated genes (ARG) and to evaluate comparative expression of these genes in normal prostate and normal prostate-related androgen-sensitive tissues that do not (or rarely) give rise to cancer.

Methods

ARG were selected in non-neoplastic adult human prostatic epithelial RWPE-1 cells stably expressing an exogenous human androgen receptor, using RNA-microarrays and validation by qRT-PCR. Expression of 48 preselected genes was quantified in tissue samples (seminal vesicles, prostate transitional zones and prostate cancers, benign prostatic hypertrophy obtained from surgical specimens) using TaqMan® low-density arrays. The diagnostic performances of these potential biomarkers were compared to that of genes known to be associated with PCa (i.e. PCA3 and DLX1).

Results and Discussion

By crossing expression studies in 26 matched PCa and normal prostate transitional zone samples, and 35 matched seminal vesicle and PCa samples, 14 genes were identified. Similarly, 9 genes were overexpressed in 15 benign prostatic hypertrophy samples, as compared to PCa samples. Overall, we selected 8 genes of interest to evaluate their diagnostic performances in comparison with that of PCA3 and DLX1. Among them, 3 genes: CRYAB, KCNMA1 and SDPR, were overexpressed in all 3 reference non-cancerous tissues. The areas under ROC curves of these genes reached those of PCA3 (0.91) and DLX1 (0.94).

Conclusions

We identified ARG with reduced expression in PCa and with significant diagnostic values for discriminating between cancerous and non-cancerous prostatic tissues, similar that of PCA3. Given their expression pattern, they could be considered as potentially protective against prostate cancer. Moreover, they could be complementary to known genes overexpressed in PCa and included along with them in multiplex diagnostic tools.

[Expressions and significances of CRABPII and E-FABP in non-small cell lung cancer]

背景与目的

细胞视黄酸结合蛋白（cellular retinoic acid-binding protein Ⅱ, CRABPⅡ）和表皮型脂肪酸结合蛋白（epidermal fatty acid-binding protein, E-FABP）作为维甲酸（retinoic acid, RA）的转运蛋白，通过RA信号传导通路，从正反两方面影响细胞的增殖和凋亡。本研究旨在探讨CRABPII和E-FABP在非小细胞肺癌（non-small cell lung cancer, NSCLC）中的表达及意义。

方法

利用组织芯片技术和免疫组织化学SP法检测54例正常肺组织、287例NSCLC原发癌组织以及103例淋巴结转移癌组织中CRABPII和E-FABP的表达。

结果

CRABPII在NSCLC原发癌组织中的表达与患者的性别、肿瘤的有无转移、TNM分期有关（P < 0.05）。E-FABP在NSCLC原发癌组织中的阳性表达率分别高于正常肺组织和淋巴结转移癌组织（P < 0.05）。在NSCLC原发癌组织中，E-FABP的表达与肿瘤的病理分级、有无转移有关（P < 0.05）。在NSCLC中，E-FABP的阳性表达较CRABPII占优势（P < 0.05），两种蛋白的差异性表达与肿瘤的大小、病理分级、有无转移、TNM分期有关（P < 0.05），瘤体愈大，肿瘤发生转移，临床分期愈晚，E-FABP的表达愈占优势。Kaplan-Meier单因素生存分析显示：CRABPII的表达、CRABPII与E-FABP的差异性表达与NSCLC患者的预后有关（P < 0.05）。

结论

E-FABP在NSCLC中高表达，其表达的增强可能与NSCLC的发生和演进有关；CRABPII可能在NSCLC的发展过程中起负向调节作用，CRABPII阴性表达患者术后生存率更高，对NSCLC患者预后的评估有一定价值。

Maintenance of genomic integrity after DNA double strand breaks in the human prostate and seminal vesicle epithelium: the best and the worst

Prostate cancer is one of the most frequent cancer types in men, and its incidence is steadily increasing. On the other hand, primary seminal vesicle carcinomas are extremely rare with less than 60 cases reported worldwide. Therefore the difference in cancer incidence has been estimated to be more than a 100,000-fold. This is astonishing, as both tissues share similar epithelial structure and hormonal cues. Clearly, the two epithelia differ substantially in the maintenance of genomic integrity, possibly due to inherent differences in their DNA damage burden and DNA damage signaling. The DNA damage response evoked by DNA double strand breaks may be relevant, as their faulty repair has been implicated in the formation of common genomic rearrangements such as TMPRSS2-ERG fusions during prostate carcinogenesis. Here, we review DNA damaging processes of both tissues with an emphasis on inflammation and androgen signaling. We discuss how benign prostate and seminal vesicle epithelia respond to acute DNA damage, focusing on the canonical DNA double strand break-induced ATM-pathway, p53 and DNA damage induced checkpoints. We propose that the prostate might be more prone to the accumulation of genetic aberrations during epithelial regeneration than seminal vesicles due to a weaker ability to enforce DNA damage checkpoints.

Deregulation of a Hox protein regulatory network spanning prostate cancer initiation and progression

PURPOSE

The aberrant activity of developmental pathways in prostate cancer may provide significant insight into predicting tumor initiation and progression, as well as identifying novel therapeutic targets. To this end, despite shared androgen-dependence and functional similarities to the prostate gland, seminal vesicle cancer is exceptionally rare.

EXPERIMENTAL DESIGN

We conducted genomic pathway analyses comparing patient-matched normal prostate and seminal vesicle epithelial cells to identify novel pathways for tumor initiation and progression. Derived gene expression profiles were grouped into cancer biomodules using a protein-protein network algorithm to analyze their relationship to known oncogenes. Each resultant biomodule was assayed for its prognostic ability against publically available prostate cancer patient gene array datasets.

RESULTS

Analyses show that the embryonic developmental biomodule containing four homeobox gene family members (Meis1, Meis2, Pbx1, and HoxA9) detects a survival difference in a set of watchful-waiting patients (n = 172, P = 0.05), identify men who are more likely to recur biochemically postprostatectomy (n = 78, P = 0.02), correlate with Gleason score (r = 0.98, P = 0.02), and distinguish between normal prostate, primary tumor, and metastatic disease. In contrast to other cancer types, Meis1, Meis2, and Pbx1 expression is decreased in poor-prognosis tumors, implying that they function as tumor suppressor genes for prostate cancer. Immunohistochemical staining documents nuclear basal-epithelial and stromal Meis2 staining, with loss of Meis2 expression in prostate tumors.

CONCLUSION

These data implicate deregulation of the Hox protein cofactors Meis1, Meis2, and Pbx1 as serving a critical function to suppress prostate cancer initiation and progression.

Contrasting DNA damage checkpoint responses in epithelium of the human seminal vesicle and prostate

BACKGROUND

Prostate and seminal vesicle are two similar hormone responsive human organs that differ dramatically in their cancer incidence. DNA damage response (DDR) is required for maintenance of genomic integrity.

METHODS

In this study we investigated the DDR and cell cycle checkpoint activation of these organs using orthotopic cultures of human surgery-derived tissues and primary cultures of isolated prostate and seminal vesicle cells.

RESULTS

We find that the activation of ATM signaling pathway by ionizing radiation (IR) was comparable in both tissues. Previously, we have shown that the prostate secretory cells express low levels of histone variant H2AX and phosphorylated H2AX (γH2AX) after IR. Here we demonstrate that H2AX levels are low also in the secretory seminal vesicle cells suggesting that this is a common phenotype of postmitotic cells. We consequently established primary epithelial cell cultures from both organs to compare their DDR. Interestingly, contrary to human prostate epithelial cells (HPEC), primary seminal vesicle epithelial cells (HSVEC) displayed effective cell cycle checkpoints after IR and expressed higher levels of Wee1A checkpoint kinase. Furthermore, HSVEC but not HPEC cells were able to activate p53 and to induce p21 cell cycle inhibitor.

DISCUSSION

Our results show that during replication, the checkpoint enforcement is more proficient in the seminal vesicle than in the prostate epithelium cells. This indicates a more stringent enforcement of DDR in replicating seminal vesicle epithelial cells, and suggests that epithelial regeneration combined with sub-optimal checkpoint responses may contribute to high frequency of genetic lesions in the prostate epithelium.

Identifying causal genes and dysregulated pathways in complex diseases

In complex diseases, various combinations of genomic perturbations often lead to the same phenotype. On a molecular level, combinations of genomic perturbations are assumed to dys-regulate the same cellular pathways. Such a pathway-centric perspective is fundamental to understanding the mechanisms of complex diseases and the identification of potential drug targets. In order to provide an integrated perspective on complex disease mechanisms, we developed a novel computational method to simultaneously identify causal genes and dys-regulated pathways. First, we identified a representative set of genes that are differentially expressed in cancer compared to non-tumor control cases. Assuming that disease-associated gene expression changes are caused by genomic alterations, we determined potential paths from such genomic causes to target genes through a network of molecular interactions. Applying our method to sets of genomic alterations and gene expression profiles of 158 Glioblastoma multiforme (GBM) patients we uncovered candidate causal genes and causal paths that are potentially responsible for the altered expression of disease genes. We discovered a set of putative causal genes that potentially play a role in the disease. Combining an expression Quantitative Trait Loci (eQTL) analysis with pathway information, our approach allowed us not only to identify potential causal genes but also to find intermediate nodes and pathways mediating the information flow between causal and target genes. Our results indicate that different genomic perturbations indeed dys-regulate the same functional pathways, supporting a pathway-centric perspective of cancer. While copy number alterations and gene expression data of glioblastoma patients provided opportunities to test our approach, our method can be applied to any disease system where genetic variations play a fundamental causal role.

Epigenetic silencing of CRABP2 and MX1 in head and neck tumors

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease affecting the epithelium of the oral cavity, pharynx and larynx. Conditions of most patients are diagnosed at late stages of the disease, and no sensitive and specific predictors of aggressive behavior have been identified yet. Therefore, early detection and prognostic biomarkers are highly desirable for a more rational management of the disease. Hypermethylation of CpG islands is one of the most important epigenetic mechanisms that leads to gene silencing in tumors and has been extensively used for the identification of biomarkers. In this study, we combined rapid subtractive hybridization and microarray analysis in a hierarchical manner to select genes that are putatively reactivated by the demethylating agent 5-aza-2'-deoxycytidine (5Aza-dC) in HNSCC cell lines (FaDu, UM-SCC-14A, UM-SCC-17A, UM-SCC-38A). This combined analysis identified 78 genes, 35 of which were reactivated in at least 2 cell lines and harbored a CpG island at their 5' region. Reactivation of 3 of these 35 genes (CRABP2, MX1, and SLC15A3) was confirmed by quantitative real-time polymerase chain reaction (PCR; fold change, >or=3). Bisulfite sequencing of their CpG islands revealed that they are indeed differentially methylated in the HNSCC cell lines. Using methylation-specific PCR, we detected a higher frequency of CRABP2 (58.1% for region 1) and MX1 (46.3%) hypermethylation in primary HNSCC when compared with lymphocytes from healthy individuals. Finally, absence of the CRABP2 protein was associated with decreased disease-free survival rates, supporting a potential use of CRABP2 expression as a prognostic biomarker for HNSCC patients.

New genomic structure for prostate cancer specific gene PCA3 within BMCC1: implications for prostate cancer detection and progression

Background

The prostate cancer antigen 3 (PCA3/DD3) gene is a highly specific biomarker upregulated in prostate cancer (PCa). In order to understand the importance of PCA3 in PCa we investigated the organization and evolution of the PCA3 gene locus.

Methods/Principal Findings

We have employed cDNA synthesis, RTPCR and DNA sequencing to identify 4 new transcription start sites, 4 polyadenylation sites and 2 new differentially spliced exons in an extended form of PCA3. Primers designed from these novel PCA3 exons greatly improve RT-PCR based discrimination between PCa, PCa metastases and BPH specimens. Comparative genomic analyses demonstrated that PCA3 has only recently evolved in an anti-sense orientation within a second gene, BMCC1/PRUNE2. BMCC1 has been shown previously to interact with RhoA and RhoC, determinants of cellular transformation and metastasis, respectively. Using RT-PCR we demonstrated that the longer BMCC1-1 isoform - like PCA3 – is upregulated in PCa tissues and metastases and in PCa cell lines. Furthermore PCA3 and BMCC1-1 levels are responsive to dihydrotestosterone treatment.

Conclusions/Significance

Upregulation of two new PCA3 isoforms in PCa tissues improves discrimination between PCa and BPH. The functional relevance of this specificity is now of particular interest given PCA3's overlapping association with a second gene BMCC1, a regulator of Rho signalling. Upregulation of PCA3 and BMCC1 in PCa has potential for improved diagnosis.

Does GATA3 act in tissue-specific pathways? A meta-analysis-based approach

The GATA3 transcription factor is expressed in many tissues such as the immune system, kidney, brain, endometrium, and mammary epithelial cells. As such it must co-ordinate a diverse transcriptional program to achieve specific outcomes in different tissues. One of the most interesting questions raised is whether GATA3 will be involved in the same pathways in every tissue or will be involved in distinct regulatory networks within different tissue types? While previous studies may imply the latter, with some known targets of GATA3 perhaps being specific to cell-type or tissue-type, the question has not been systematically addressed until now. With the advent of techniques such as co-expression meta-analysis a better understanding of the pathway partners of GATA3 can be obtained and specifically the partners within different tissue types can be found, yielding leads for future studies. Here, a recent technique of meta-analysis from the Oncomine database has been employed to probe this very question. Data obtained implies that GATA3 is involved in distinct pathways in different tissue types.