Fingerprinting the diseased prostate: associations between BPH and prostate cancer

Identification of hub genes predicting the development of prostate cancer from benign prostate hyperplasia and analyzing their clinical value in prostate cancer by bioinformatic analysis

Prostate cancer (PCa) and benign prostate hyperplasia (BPH) are commonly encountered diseases in males. Studies showed that genetic factors are responsible for the occurrences of both diseases. However, the genetic association between them is still unclear. Gene Expression Omnibus (GEO) database can help determine the differentially expressed genes (DEGs) between BPH and PCa. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were utilized to find pathways DEGs enriched. The STRING database can provide a protein-protein interaction (PPI) network, and find hub genes in PPI network. R software was used to analyze the clinical value of hub genes in PCa. Finally, the function of these hub genes was tested in different databases, clinical samples, and PCa cells. Fifteen up-regulated and forty-five down-regulated genes were found from GEO database. Seven hub genes were found in PPI network. The expression and clinical value of hub genes were analyzed by The Cancer Genome Atlas (TCGA) data. Except CXCR4, all hub genes expressed differently between tumor and normal samples. Exclude CXCR4, other hub genes have diagnostic value in predicting PCa and their mutations can cause PCa. The expression of CSRP1, MYL9 and SNAI2 changed in different tumor stage. CSRP1 and MYH11 could affect disease-free survival (DFS). Same results reflected in different databases. The expression and function of MYC, MYL9, and SNAI2, were validated in clinical samples and PCa cells. In conclusion, seven hub genes among sixty DEGs may be achievable targets for predicting which BPH patients may later develop PCa and they can influence the progression of PCa.

NELL2 modulates cell proliferation and apoptosis via ERK pathway in the development of benign prostatic hyperplasia

Benign prostatic hyperplasia (BPH) is a quite common illness but its etiology and mechanism remain unclear. Neural epidermal growth factor-like like 2 (NELL2) plays multifunctional roles in neural cell growth and is strongly linked to the urinary tract disease. Current study aims to determine the expression, functional activities and underlying mechanism of NELL2 in BPH. Human prostate cell lines and tissues from normal human and BPH patients were utilized. Immunohistochemical staining, immunofluorescent staining, RT-polymerase chain reaction (PCR) and Western blotting were performed. We further generated cell models with NELL2 silenced or overexpressed. Subsequently, proliferation, cycle, and apoptosis of prostate cells were determined by cell counting kit-8 (CCK-8) assay and flow cytometry analysis. The epithelial-mesenchymal transition (EMT) and fibrosis process were also analyzed. Our study revealed that NELL2 was up-regulated in BPH samples and localized in the stroma and the epithelium compartments of human prostate tissues. NELL2 deficiency induced a mitochondria-dependent cell apoptosis, and inhibited cell proliferation via phosphorylating extracellular signal-regulated kinase 1/2 (ERK1/2) activation. Additionally, suppression of ERK1/2 with U0126 incubation could significantly reverse NELL2 deficiency triggered cell apoptosis. Consistently, overexpression of NELL2 promoted cell proliferation and inhibited cell apoptosis. However, NELL2 interference was observed no effect on EMT and fibrosis process. Our novel data demonstrated that up-regulation of NELL2 in the enlarged prostate could contribute to the development of BPH through enhancing cell proliferation and inhibited a mitochondria-dependent cell apoptosis via the ERK pathway. The NELL2-ERK system might represent an important target to facilitate the development of future therapeutic approaches in BPH.

Diagnostic and prognostic value of serum miR-15a and miR-16-1 expression among egyptian patients with prostate cancer

Prostate cancer (PCa) is considered the most common malignancy in men. The aim of this study is to assess the role of serum miR-15a and miR-16-1 expression in PCa development, diagnosis and prognosis aiming to find a specific noninvasive biomarker. This study comprised 70 patients with PCa, 70 patients complaining of benign prostatic hyperplasia (BPH), 30 patients with chronic prostatitis and 70 controls. Circulating miR-15a and miR-16-1 expression was detected by real-time polymerase chain reaction. Prostate specific antigen levels were measured by enzyme-linked immunosorbent assay. The expression levels of serum miR-15a were decreased in PCa patients compared with controls, chronic prostatitis and BPH patients (0.43 ± 0.12, 1.7 ± 0.76, 1.56 ± 0.34 and 1.53 ± 0.65, respectively). The expression levels of serum miR-16-1 were decreased in PCa patients compared with controls, chronic prostatitis and BPH patients (0.55 ± 0.23, 2.15 ± 0.87, 2.08 ± 0.54 and 1.96 ±0.61, respectively). Downregulation of miR-15a and miR-16-1 correlated with higher Gleason score (P = 0.002 and P = 0.006, respectively), higher tumor stage (P = 0.001 and P = 0.01, respectively), PCa metastasis (P = 0.002 and P = 0.025, respectively) and lymph node involvement (P = 0.02 and P = 0.007, respectively). Moreover, Receiver operating characteristic curve analysis revealed that combined miR-15a/miR-16-1 and PSA increased the sensitivity and specificity for the diagnosis of PCa (97.1% and 94.3%, respectively) more than prostate specific antigen alone (82.9% sensitivity and 75.7% specificity). Combined serum miR-15a/miR-16-1 expression and PSA level can be used as promising specific noninvasive biomarkers in the diagnosis and prognosis of PCa better than prostate specific antigen alone. © 2018 IUBMB Life, 70(5):437-444, 2018.

Screening key genes for abdominal aortic aneurysm based on gene expression omnibus dataset

Background

Abdominal aortic aneurysm (AAA) is a common cardiovascular system disease with high mortality. The aim of this study was to identify potential genes for diagnosis and therapy in AAA.

Methods

We searched and downloaded mRNA expression data from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) from AAA and normal individuals. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, transcriptional factors (TFs) network and protein-protein interaction (PPI) network were used to explore the function of genes. Additionally, immunohistochemical (IHC) staining was used to validate the expression of identified genes. Finally, the diagnostic value of identified genes was accessed by receiver operating characteristic (ROC) analysis in GEO database.

Results

A total of 1199 DEGs (188 up-regulated and 1011 down-regulated) were identified between AAA and normal individual. KEGG pathway analysis displayed that vascular smooth muscle contraction and pathways in cancer were significantly enriched signal pathway. The top 10 up-regulated and top 10 down-regulated DEGs were used to construct TFs and PPI networks. Some genes with high degrees such as NELL2, CCR7, MGAM, HBB, CSNK2A2, ZBTB16 and FOXO1 were identified to be related to AAA. The consequences of IHC staining showed that CCR7 and PDGFA were up-regulated in tissue samples of AAA. ROC analysis showed that NELL2, CCR7, MGAM, HBB, CSNK2A2, ZBTB16, FOXO1 and PDGFA had the potential diagnostic value for AAA.

Conclusions

The identified genes including NELL2, CCR7, MGAM, HBB, CSNK2A2, ZBTB16, FOXO1 and PDGFA might be involved in the pathology of AAA.

CAFÉ-Map: Context Aware Feature Mapping for mining high dimensional biomedical data

Feature selection and ranking is of great importance in the analysis of biomedical data. In addition to reducing the number of features used in classification or other machine learning tasks, it allows us to extract meaningful biological and medical information from a machine learning model. Most existing approaches in this domain do not directly model the fact that the relative importance of features can be different in different regions of the feature space. In this work, we present a context aware feature ranking algorithm called CAFÉ-Map. CAFÉ-Map is a locally linear feature ranking framework that allows recognition of important features in any given region of the feature space or for any individual example. This allows for simultaneous classification and feature ranking in an interpretable manner. We have benchmarked CAFÉ-Map on a number of toy and real world biomedical data sets. Our comparative study with a number of published methods shows that CAFÉ-Map achieves better accuracies on these data sets. The top ranking features obtained through CAFÉ-Map in a gene profiling study correlate very well with the importance of different genes reported in the literature. Furthermore, CAFÉ-Map provides a more in-depth analysis of feature ranking at the level of individual examples.

AVAILABILITY

CAFÉ-Map Python code is available at: http://faculty.pieas.edu.pk/fayyaz/software.html#cafemap . The CAFÉ-Map package supports parallelization and sparse data and provides example scripts for classification. This code can be used to reconstruct the results given in this paper.

Expression and regulatory effects on cancer cell behavior of NELL1 and NELL2 in human renal cell carcinoma

Neural epidermal growth factor-like like (NELL) 1 and 2 constitute a family of multimeric and multimodular extracellular glycoproteins. Although the osteogenic effects of NELL1 and functions of NELL2 in neural development have been reported, their expression and functions in cancer are largely unknown. In this study, we examined expression of NELL1 and NELL2 in renal cell carcinoma (RCC) using clinical specimens and cell lines. We show that, whereas NELL1 and NELL2 proteins are strongly expressed in renal tubules in non-cancerous areas of RCC specimens, their expression is significantly downregulated in cancerous areas. Silencing of NELL1 and NELL2 mRNA expression was also detected in RCC cell lines. Analysis of NELL1/2 promoter methylation status indicated that the CpG islands in the NELL1 and NELL2 genes are hypermethylated in RCC cell lines. NELL1 and NELL2 bind to RCC cells, suggesting that these cells express a receptor for NELL1 and NELL2 that can transduce signals. Furthermore, we found that both NELL1 and NELL2 inhibit RCC cell migration, and NELL1 further inhibits RCC cell adhesion. These results suggest that silencing of NELL gene expression by promoter hypermethylation plays roles in RCC progression by affecting cancer cell behavior.

Endogenous molecular-cellular hierarchical modeling of prostate carcinogenesis uncovers robust structure

We explored endogenous molecular-cellular network hypothesis for prostate cancer by constructing relevant endogenous interaction network model and analyzing its dynamical properties. Molecular regulations involved in cell proliferation, apoptosis, differentiation and metabolism are included in a hierarchical mathematical modeling scheme. This dynamical network organizes into multiple robust functional states, including physiological and pathological ones. Some states have characteristics of cancer: elevated metabolic and immune activities, high concentration of growth factors and different proliferative, apoptotic and adhesive behaviors. The molecular profile of calculated cancer state agrees with existing experiments. The modeling results have additional predictions which may be validated by further experiment: 1) Prostate supports both stem cell like and liver style proliferation; 2) While prostate supports multiple cell types, including basal, luminal and endocrine cell type differentiated from its stem cell, luminal cell is most likely to be transformed malignantly into androgen independent type cancer; 3) Retinoic acid pathway and C/EBPα are possible therapeutic targets.

Association of symptomatic benign prostatic hyperplasia and prostate cancer: results from the prostate cancer prevention trial

This study examined the association between symptomatic benign prostatic hyperplasia (BPH) and prostate cancer risk in 5,068 placebo-arm participants enrolled in the Prostate Cancer Prevention Trial (1993-2003). These data include 1,225 men whose cancer was detected during the 7-year trial--556 detected for cause (following abnormal prostate-specific antigen or digital rectal examination) and 669 detected not for cause (without indication), as well as 3,843 men who had biopsy-proven absence of prostate cancer at the trial end. Symptomatic BPH was assessed hierarchically as self-report of surgical or medical treatment, moderately severe symptoms (International Prostate Symptom Score >14), or physician diagnosis, and analyses were completed by BPH status at baseline (prevalent) or BPH prior to cancer diagnosis or study end (prevalent plus incident). Controlled for age, race, and body mass index, neither prevalent (risk ratio = 1.03, 95% confidence interval: 0.92, 1.14) nor prevalent plus incident (risk ratio = 0.96, 95% confidence interval: 0.87, 1.06) symptomatic BPH was associated with prostate cancer risk. This lack of association was consistent across subgroups defined by type of BPH-defining event (treatment, symptoms, or physician diagnosis), prompt for prostate cancer diagnosis, and prostate cancer grade. This study provides the strongest evidence to date that BPH does not increase the risk of prostate cancer.

The natural compounds atraric acid and N-butylbenzene-sulfonamide as antagonists of the human androgen receptor and inhibitors of prostate cancer cell growth

Extracts from the plant Pygeum africanum are widely used in the therapy of benign prostate hyperplasia (BPH) and in combinational therapy for prostate cancer, the second leading cause of cancer death and the mostly diagnosed form of cancer in men. The androgen receptor (AR) plays a crucial role in the development of the prostate as well as in prostate diseases. Even though the extracts from P. africanum are considered as beneficial for prostate diseases in clinical trials, and some active compounds for treatment of BPH could be identified, compounds responsible for AR inhibition and the molecular mechanism for inhibition of prostatitis need to be identified. Recently, atraric acid and N-butylbenzene-sulfonamide were isolated from a selective dichlormethane extract of P. africanum as two novel AR antagonistic compounds. The molecular mechanisms of AR inhibition were analyzed and are summarized here. Both compounds are the first known natural, complete and specific AR antagonist.

Novel methods to identify biologically relevant genes for leukemia and prostate cancer from gene expression profiles

Background

High-throughput microarray experiments now permit researchers to screen thousands of genes simultaneously and determine the different expression levels of genes in normal or cancerous tissues. In this paper, we address the challenge of selecting a relevant and manageable subset of genes from a large microarray dataset. Currently, most gene selection methods focus on identifying a set of genes that can further improve classification accuracy. Few or none of these small sets of genes, however, are biologically relevant (i.e. supported by medical evidence). To deal with this critical issue, we propose two novel methods that can identify biologically relevant genes concerning cancers.

Results

In this paper, we propose two novel techniques, entitled random forest gene selection (RFGS) and support vector sampling technique (SVST). Compared with results from six other methods developed in this paper, we demonstrate experimentally that RFGS and SVST can identify more biologically relevant genes in patients with leukemia or prostate cancer. Among the top 25 genes selected using SVST method, 15 genes were biologically relevant genes in patients with leukemia and 13 genes were biologically relevant genes in patients with prostate cancer. Meanwhile, the RFGS method, while less effective than SVST, still identified an average of 9 biologically relevant genes in both leukemia and prostate cancers. In contrast to traditional statistical methods, which only identify less than 8 genes in patients with leukemia and less than 8 genes in patients with prostate cancer, our methods yield significantly better results.

Conclusions

Our proposed SVST and RFGS methods are novel approaches that can identify a greater number of biologically relevant genes. These methods have been successfully applied to both leukemia and prostate cancers. Research in the fields of biology and medicine should benefit from the identification of biologically relevant genes by confirming recent discoveries in cancer research or suggesting new avenues for exploration.

Joint effects of inflammation and androgen metabolism on prostate cancer severity

Multiple pathways of prostate carcinogenesis have been proposed, including those involving androgen metabolism and inflammation. These pathways are not independent, and may act together in prostate cancer etiology: androgens promote both inflammatory processes and serve as mitogens in prostate tumor growth. To explore the possible joint effects of these pathways in prostate cancer severity, we studied 1,090 Caucasian prostate cancer cases to evaluate whether tumor severity is influenced by a history of benign prostatic hyperplasia (BPH) interacting with genotypes involved in inflammation or androgen metabolism including MSR1, RNASEL, AR, CYP3A4, CYP3A43, CYP3A5 and SRD5A2. We observed a statistically significant interaction between a number of genotypes and BPH. After considering the potential for false positive associations, the only remaining significant associations involved CYP3A43 P340A genotypes and history of BPH on both Gleason grade (interaction p-value = 0.026) and tumor stage (interaction p-value = 0.017). These results suggest that androgen metabolism may act in concert with inflammatory phenotypes such as BPH in determining prostate cancer severity.

Effective gene selection method with small sample sets using gradient-based and point injection techniques

Microarray gene expression data usually consist of a large amount of genes. Among these genes, only a small fraction is informative for performing cancer diagnostic test. This paper focuses on effective identification of informative genes. We analyze gene selection models from the perspective of optimization theory. As a result, a new strategy is designed to modify conventional search engines. Also, as overfitting is likely to occur in microarray data because of their small sample set, a point injection technique is developed to address the problem of overfitting. The proposed strategies have been evaluated on three kinds of cancer diagnosis. Our results show that the proposed strategies can improve the performance of gene selection substantially. The experimental results also indicate that the proposed methods are very robust under all the investigated cases.

The ageing male reproductive tract

Ageing of the male reproductive system is characterized by changes in the endocrine system, hypogonadism, erectile dysfunction and proliferative disorders of the prostate gland. Stochastic damage accumulating within ageing leads to progressive dysregulation at each level of the hypothalamic-pituitary-gonadal (HPG) axis and in local auto/paracrine interactions, thereby inducing morphological changes in reproductive target organs, such as the prostate, testis and penis. Despite age-related changes in the HPG axis, endocrine functions are generally sufficient to maintain fertility in elderly men. Ageing of the male reproductive system can give rise to clinically relevant manifestations, such as benign prostatic hyperplasia (BPH), prostate cancer (PCa) and erectile dysfunction (ED). In this review, we discuss morphological/histological changes occurring in these organs and current views and concepts of the underlying pathology. Moreover, we emphasize the molecular/cellular pathways leading to reduced testicular/penile function and proliferative disorders of the prostate gland.

Is benign prostatic hyperplasia (BPH) an immune inflammatory disease?

OBJECTIVES

Chronic inflammation has been documented for years in benign prostatic hyperplasia (BPH), but only now has it become evident as a major factor in disease progression. This review highlights the immunologic key features of chronic inflammation in BPH and the present interpretation of these changes in the development and progression of BPH.

RESULTS

Almost all BPH specimens show inflammatory infiltrates at histologic examination, but correlation to bacterial or other foreign antigens has not been established. Recognition of prostate secretion products by autoreactive T cells and animal models on experimental prostatitis demonstrate an autoimmune component to chronic inflammation. The infiltrate consists predominantly of chronically activated CD4(+) T lymphocytes, which are permanently recruited to prostate tissue via elevated expression of interleukin 15 (IL-15) and interferon gamma (IFN-gamma), proinflammatory cytokines produced by smooth muscle and T cells, respectively. With the appearance of infiltrates, T cell-derived cytokine production of IFN-gamma, IL-2, and transforming growth factor beta increases, the former two ultimately reaching 10-fold and the latter 2-fold higher levels in fully developed BPH than in normal prostates. As "mature" BPH nodules develop, IL-4 and IL-13 expression increases >2-fold, corresponding to a T-helper (Th)0/Th2 cytokine pattern. Dysregulation of the immune response in BPH may occur via elevated expression of proinflammatory IL-17, which stimulates a multifold production of IL-6 and IL-8, key executors of stromal growth in BPH.

CONCLUSIONS

These data strongly suggest that BPH is an immune inflammatory disease. Unravelling the specific nature of immune dysregulation may help design novel drugs with these specific targets in mind.

Gene expression profiling of the human prostate zones

OBJECTIVE

To investigate differences in gene expression in different zones of the prostate by microarray analyses, to better understand why aggressive tumours predominantly occur in the peripheral zone (PZ), whereas benign prostatic hyperplasia (BPH) occurs almost exclusively in the transition zone (TZ).

MATERIALS AND METHODS

Expression profiling of both prostate zones was done by microarray analysis. Reverse transcription-polymerase chain reaction (RT-PCR) of the top 18 genes confirmed the microarray analyses. RT-PCR with common cell-type markers indicated that the differential expression between the zones was not caused by an unequal distribution of different cell types. Primary stromal and epithelial prostate cells were used to study cell type expression in the 12 highest differentially expressed zonal-specific genes.

RESULTS

In all, 346 genes were identified as preferentially expressed in the TZ or PZ. A few of the TZ-specific genes, including ASPA, FLJ10970 and COCH, were also stroma-specific. Comparisons with other microarray studies showed that gene expression profiles of prostate cancer and BPH correlate with the expression profiles of the PZ and TZ, respectively.

CONCLUSION

Gene expression differs between the PZ and TZ of the prostate, and stromal-epithelial interactions might be responsible for the distinct zonal localization of prostate diseases.

BENIGN PROSTATIC HYPERPLASIA CELL LINE VIABILITY AND MODULATION OF JM-27 BY DOXAZOSIN AND IBUPROFEN

PURPOSE

Benign prostatic hyperplasia (BPH) is among the most common diseases affecting quality of life in older men. Despise intense research efforts to our knowledge the genetic mechanisms underlying the BPH disease process and therapeutic markers needed to determine patient responsiveness to a particular form of pharmacological therapy are still not identified. This has slowed the development of new therapeutic agents for the treatment of BPH.

MATERIALS AND METHODS

We investigated the cellular effects of certain drugs on BPH. Besides doxazosin, which is the prevailing drug to treat BPH, the effect of ibuprofen was examined as a new therapeutic approach due to strong evidence of a correlation between BPH and inflammation.

RESULTS

This study showed that doxazosin as well as ibuprofen significantly decreases cell viability and induced apoptosis in 267 B1 cells as well as in BPH-1 cells. In addition, we observed that the administration of doxazosin and ibuprofen to BPH-1 cells decreased the expression of JM-27, a protein particularly expressed in prostate that is highly up-regulated in symptomatic BPH.

CONCLUSIONS

Our findings suggest that ibuprofen may be a new therapeutic target for the treatment of BPH. Further research must be done to investigate the potential use of ibuprofen in patients with BPH and examine if JM-27 expression in patients with BPH may stratify individuals who may be most responsive to pharmacological treatment.