DD3(PCA3)-based molecular urine analysis for the diagnosis of prostate cancer

Nucleic acid-based marker approaches to urologic cancers

There are numerous molecular modifications known to occur in cancer. New nucleic acid-based biomarkers provide a unique approach to patient management in urologic oncology. Malignant transformation of a normal cell requires a series of epigenetic and genetic changes or "hits." Epigenetics produced by deoxyribonucleic acid methylation, adding a methyl group to the fifth position of cytosine within CpG dinucleotides, are important players in deoxyribonucleic acid repair, genome instability, and regulation of chromatin structure. Genetic alterations in cancer can include mutations, chromosome deletions, insertions, amplifications, and translocations. In addition, the modifications of telomeres are critical to the maintenance of chromatin structure, transcription, and cell function in cancer. We review only nucleic acid-based molecular biomarkers in urologic oncology that can assist the clinician in establishing the diagnosis of disease, or that can predict the behavior of the disease or the patient's survival.

Novel homogenous time-resolved fluorometric RT-PCR assays for quantification of PSA and hK2 mRNAs in blood

OBJECTIVES

The purpose of this study was to design, validate, and optimize internally standardized real-time quantitative RT-PCR assays and to identify and avoid problems with assay reliability and examine the impact of an exogenous internal standard.

DESIGN AND METHODS

The model system consisted of internally standardized quantitative real-time RT-PCR assays specific for PSA and hK2 mRNA based on time-resolved fluorometric detection of lanthanide chelates.

RESULTS

Reproducibility was best when large copy numbers (>5000 per milliliter blood) were analyzed. Addition of an exogenous target-mimicking internal standard had no significant effect on the reproducibility of the method, but increased the calculated copy numbers by an average of 2-fold.

CONCLUSIONS

We developed an internally standardized, specific and reproducible real-time RT-PCR analysis method for PSA and hK2 mRNA in circulating cells in the bloodstream. Both PSA and hK2 assays are sufficiently sensitive to detect two LNCaP cells per milliliter whole blood.

Characterization of frequently deleted 6q locus in prostate cancer

The long arm of chromosome 6 is frequently deleted in diverse human neoplasms. Our previous study showed a minimum deletion region between markers D6S1056 and D6S300 on chromosome 6q in primary prostate cancer (CaP). In this study, we further refined a 200-kb minimal region of deletion (6qTSG1) centered around D6S1013 marker. The 6qTSG1 transcripts contained complex multiple splicing variants with low or absent expression in CaP cells. None of the transcripts identified contained open reading frames that code for a protein in the NCBI database. The expression of 6qTSG transcripts revealed interesting hormonal regulation relevant to CaP biology. Expression of 6q TSG transcript was induced in LNCaP cells that were cultured in charcoal-stripped serum medium suggesting an upregulation of 6qTSG transcript by androgen ablation and cell growth inhibition/apoptosis. Induction of 6qTSG1 expression in response to androgen ablation was abrogated in androgen-independent derivatives of LNCaP cells. In summary, we have defined a candidate CaP suppressor locus on chromosome 6q16.1, and deletions of this locus are frequently associated with prostate tumorigenesis. In the light of emerging role of noncoding RNAs in cancer biology including CaP, future investigations of 6qTSG11 locus is warranted.

Urinary markers for prostate cancer

Prostate cancer is the commonest solid-organ malignancy to affect men in Europe and the USA; it is estimated that one in six men will develop this cancer in their lifetime. Current screening relies on a digital rectal examination with a serum prostate-specific antigen test. Novel urinary diagnostic tests are potentially interesting screening tools for this disease. We examined published reports assessing the use of urinary markers for the diagnosis of prostate cancer. Using a PubMed-based search we identified studies of urinary markers for prostate cancer published from 1985 to February 2006 using the search terms 'urine', 'marker' and 'prostate cancer'. Studies to date have used small cohorts and relied on prostatic biopsies to provide histology. The sensitivity and specificity of markers are wide ranging but with only a few studies published on each putative marker it is difficult to assess their potential impact. Using urinary biomarkers for prostate cancer is a relatively novel diagnostic approach; they are appealing as a screening test because they are not invasive. Further work is needed to identify and validate 'signature markers' indicative of prostatic malignancy. The newer proteomic platforms are promising biomarker discovery tools that might uncover the next generation of urinary biomarkers.

Marqueurs biologiques du cancer de la prostate

Screening for prostate cancer is currently based on the assessment of blood prostate specific antigen (PSA). Although PSA was shown to be an adequate tool in prostate cancer screening, beginning from 4.0 ng/mL, its specificity is less significant. In men with a PSA between 4.0 and 10 ng/mL its predictive value is low. Therefore, there is a need for new instruments likely to improve the specificity of blood PSA levels between 4.0 and 10 ng/mL and the screening for prostate cancer in subjects with low PSA. Recent data are reviewed.

Molecular markers of prostate cancer

Although prostate-specific antigen (PSA) has evolved as a very useful tool for detection of prostate cancer, there remains an urgent need for more accurate biomarkers to diagnose prostate cancer and predict cancer-related outcomes. Recent advances in the study of proteomics and high throughput techniques have led to the discovery of many potential biomarkers for prostate cancer. This article briefly reviews the current status of PSA testing and discusses several candidate protein biomarkers for prostate cancer, as well as highlighting some recent proteomic discoveries with the potential to supplement or even replace PSA for the diagnosis and prognosis of prostate cancer.

Molecular markers in the diagnosis of prostate cancer

The genetic alterations leading to prostate cancer are gradually being discovered. A wide variety of genes have been associated with prostate cancer development as well as tumor progression. Knowledge of gene polymorphisms associated with disease aid in the understanding of important pathways involved in this process and may result in the near future in clinical applications. Urinary molecular markers will soon be available to aid in the decision of repeat prostate biopsies. Recent findings suggest the importance of androgen signaling in disease development and progression. The further understanding of interaction of inflammation, diet, and genetic predisposition will improve risk stratification in the near future.

Emerging biomarkers in prostate cancer

Biomarkers may be proteins, RNA, DNA, autoantibodies or molecules that reliably diagnose cancer or serve as markers of prognosis. Prognosis is particularly important in prostate cancer, a disease many ‘die with’, but which kills only a minority of affected men. Prostate-specific antigen is widely used in screening for prostate cancer and has a significant false-positive rate, which leads to unnecessary biopsies, cost and anxiety. There is also a notable false-negative rate for prostate-specific antigen, with a significant number of high-grade tumors identified in men with a ‘normal’ prostate-specific antigen. Discovery and validation of improved diagnostic biomarkers is necessary. Biomarkers that would distinguish aggressive from more indolent forms of prostate cancer may be even more urgently required. High-throughput technologies that assay proteins, metabolites, DNA and RNA are generating candidate markers.

Prostate cancer detected by uPM3: radical prostatectomy findings

uPM3 is the first urine-based genetic test that is highly specific for detecting prostate cancer. The histopathologic characteristics of uPM3-detected cancer in radical prostatectomy specimens have not been previously described. We evaluated a consecutive series of radical prostatectomies to determine the extent, zonal distribution and other features of prostate cancer following uPM3 detection. A total of 24 whole-mounted, totally embedded radical prostatectomy specimens were evaluated. All patients had clinically localized cancer and none received preoperative therapy. Zonal location of cancer, distance to the urethra, cancer volume, Gleason grade and multicentricity were recorded; volume of cancer was measured using the grid-counting method. Patients ranged in age from 43 to 75 years (mean 65 years). In 21/24 cases, cancer involved the transition and peripheral zones and was multicentric (87%). Mean cancer volume was 3.96 cm3 (range 0.08-16.86 cm3). Mean distance to the urethra was 0.50 cm for the closest cancer and 0.61 cm for the most distant cancer. Mean Gleason score was 7 (range 5-9); pathologic stage was pT2 for 17 cases and pT3 for seven cases. The uPM3 is an independent and specific biomarker that detects prostate cancers of similar volume, location, extent and grade as other tests for early detection. uPM3 does not preferentially identify large or aggressive prostate cancers.

APTIMA PCA3 molecular urine test: development of a method to aid in the diagnosis of prostate cancer

BACKGROUND

Prostate cancer gene 3 (PCA3) encodes a prostate-specific mRNA that has shown promise as a prostate cancer diagnostic tool. This report describes the characterization of a prototype quantitative PCA3-based test for whole urine.

METHODS

Whole-urine specimens were collected after digital rectal examination from 3 groups: men scheduled for prostate biopsy (n = 70), healthy men (<45 years of age with no known prostate cancer risk factors; n = 52), and men who had undergone radical prostatectomy (n = 21). PCA3 and prostate-specific antigen (PSA) mRNAs were isolated, amplified, and quantified by use of Gen-Probe DTS400 Systems. Prostate biopsy results were correlated with the PCA3/PSA mRNA ratio, and PSA mRNA concentrations were used to normalize PCA3 signals and confirm the yield of prostate-specific RNA. Assay precision, specimen stability, and mRNA yield were also evaluated.

RESULTS

The specimen informative rate (fraction of specimens yielding sufficient RNA for analysis) was 98.2%. In this clinical research study, ROC curve analysis of prebiopsy specimens yielded an area under the curve of 0.746; sensitivity was 69% and specificity 79%. Serum PSA assay specificity was 28% for this same group. PCA3 and PSA mRNAs were undetectable in postprostatectomy specimens except for one man with recurrent prostate cancer. Assay interrun CVs were < or =12%. Both mRNAs were stable in processed urine up to 5 days at 4 degrees C and after 5 freeze-thaw cycles.

CONCLUSION

The APTIMA PCA3 assay combines simple specimen processing with precise assays and existing instruments and could add specificity to the current algorithm for prostate cancer diagnosis.

Urine markers as possible tools for prostate cancer screening: review of performance characteristics and practicality

BACKGROUND

In recent years, an increasing number of urine-based tests have been proposed as potential screening tests for prostate cancer. The goal of this review was to summarize the current status of evidence regarding performance characteristics of the proposed tests and their practicality under screening conditions.

METHOD

Relevant articles published up to and including May 2005 were identified in the PubMed database. At least 10 cases and 10 controls had to be analyzed for a study to be included in the review. Data concerning the study population, performance characteristics, and the collection and processing of urine samples were extracted from the reviewed articles.

RESULTS

In all, 34 retrospective studies evaluating 21 different markers complied with the inclusion criteria. Most of the studies were rather small and included heterogeneous clinical study populations. Promising results were reported for a few markers in single studies, but they have often not been replicated in subsequent larger studies. Some of the more promising results were obtained with 24-h urines or with specimen-handling procedures that might be difficult to perform under screening conditions.

CONCLUSIONS

Larger studies with a prospective design are required to confirm promising findings regarding performance characteristics of some novel markers recently reported in mostly small studies. Future studies should also pay particular attention to the practicality of the markers under screening conditions.

Regulatory RNAs in mammals

Recent years have brought a dramatic change in our understanding of the role of ribonucleic acids (RNAs) within the cell. In addition to the already well-known classes of RNAs that take part in the transmission of genetic information from DNA to proteins, a new highly heterogeneous group of RNA molecules has emerged. The regulatory nonprotein-coding RNAs (npcRNAs) have been shown to be involved in modulation of gene expression on both the transcriptional and post-transcriptional level. They participate in mechanisms of chromatin modification, regulation of transcription factor activity, and influencing mRNA stability, processing, and translation. npcRNAs are key factors in genetic imprinting, dosage compensation of X-chromosome-linked genes, and many processes of differentiation and development.

Molecular prostate cancer pathology: current issues and achievements

Recent developments in the field of molecular techniques have provided new tools that have led to the discovery of many new promising biomarkers for prostate cancer. These biomarkers may be instrumental in the development of new tests that will have a high specificity for the diagnosis and prognosis of prostate cancer. A biomarker is defined as a molecular test that provides additional information to currently available clinical and pathological tests. Biomarkers should be reproducible (both within and between institutes) and have an impact on clinical management. For diagnostic purposes it is important that potential biomarkers are tested in terms of tissue specificity and their discrimination potential between prostate cancer, normal prostate and benign prostatic hyperplasia. The results of (multiple) biomarker-based assays may enhance the specificity of cancer detection. There is an urgent need for molecular prognostic biomarkers for predicting the biological behavior and outcome of cancer.

Validation of molecular targets in prostate cancer

As prostate cancer is not a single disease, it is important to identify the pivotal pathway in the patient being treated. The molecular environment is the site of current oncological research to define new therapeutic targets for hormone-refractory disease, offering the potential to eventually individualize treatment through stratification of pathways. Targets may be validated either phenotypically (e.g. androgen receptor, cadherin) or functionally (e.g. prostate cancer-specific genes). In addition, several other candidates are potentially suitable, while others await discovery. Important initial steps have been made in the search for prostate cancer stem cells; identifying stem cells and the stromal, hormonal, and other signalling molecules that influence their behaviour would have important implications for managing prostate cancer. Although individual therapeutic pathways might be ineffective in a particular molecular environment, combinations of approaches might be capable of producing synergistic effects. A multimodal approach thus might be the best solution. Determining where best to search for a molecular target, and validating whether the target is associated with a sufficiently aggressive malignant process to justify further study is difficult, but the potential benefits are enormous.

PSGR2, a novel G-protein coupled receptor, is overexpressed in human prostate cancer

The G-protein coupled receptors (GPCRs) recognize a large variety of extracellular molecules (such as hormones, neurotransmitters, growth and developmental factors) and several sensory messages (such as light, odors and pain). GPCRs and their signal transduction pathway represent important specific targets for a variety of human diseases. To investigate the potential roles of GPCRs in human normal prostate and prostate cancers, we identified and characterized a novel human G-protein coupled receptor, PSGR2, which is highly overexpressed in human prostate cancers. Although PSGR2 shares sequence homology with human olfactory G-protein coupled receptors, the expression of PSGR2 is highly restricted to human prostate tissue, and no expression was detected in 22 normal and 10 tumor tissues examined using Northern blot and PCR analysis. Furthermore, we investigated the expression levels of PSGR2 in 133 human prostate samples with real-time quantitative reverse transcription-PCR and in situ hybridization method. We demonstrated that PSGR2 expression increased significantly in human high grade prostate intraepithelial neoplasia (PIN) and prostate cancers (approximately 10-fold) as compared to normal and BPH (benign prostatic hyperplasia) tissues (p < 0.001), suggesting PSGR2 may play an important role in human prostate cancer development and progression. Together, our results suggest that PSGR2 is a novel prostate specific G-protein coupled receptor and may be useful as a tissue marker and molecular target for the early detection and treatment of human prostate cancers.

Innovations in serum and urine markers in prostate cancer current European research in the P-Mark project

An overview is given of serum and urine prostate cancer markers that are currently under investigation and subsequently the P-Mark project is introduced. There are many markers showing promise to overcome the limitations of prostate specific antigen (PSA). Eventually, these markers should be able to increase the specificity in diagnosis, differentiate between harmless and aggressive disease and identify progression towards androgen independence at an early stage. In the P-Mark project, several recently developed, promising markers will be evaluated using clinically well-defined biorepositories. Following successful evaluation, these markers will be validated on a sample set derived from two large, European, prostate cancer studies and used for the identification of special risk groups in the general population. In addition, novel markers will be identified in the same biorepositories by different mass spectrometry techniques.

Use of multiple biomarkers for a molecular diagnosis of prostate cancer

The identification of biomarkers capable of providing a reliable molecular diagnostic test for prostate cancer (PCa) is highly desirable clinically. We describe here 4 biomarkers, UDP-N-Acetyl-alpha-D-galactosamine transferase (GalNAc-T3; not previously associated with PCa), PSMA, Hepsin and DD3/PCA3, which, in combination, distinguish prostate cancer from benign prostate hyperplasia (BPH). GalNAc-T3 was identified as overexpressed in PCa tissues by microarray analysis, confirmed by quantitative real-time PCR and shown immunohistochemically to be localised to prostate epithelial cells with higher expression in malignant cells. Real-time quantitative PCR analysis across 21 PCa and 34 BPH tissues showed 4.6-fold overexpression of GalNAc-T3 (p = 0.005). The noncoding mRNA (DD3/PCA3) was overexpressed 140-fold (p = 0.007) in the cancer samples compared to BPH tissues. Hepsin was overexpressed 21-fold (p = 0.049, whereas the overexpression for PSMA was 66-fold (p = 0.047). When the gene expression data for these 4 biomarkers was combined in a logistic regression model, a predictive index was obtained that distinguished 100% of the PCa samples from all of the BPH samples. Therefore, combining these genes in a real-time PCR assay represents a powerful new approach to diagnosing PCa by molecular profiling. (Supplemental material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat/index.html.)

Clinical relevance of genetic instability in prostatic cells obtained by prostatic massage in early prostate cancer

We investigated whether genetic lesions such as loss of heterozygosity (LOH) are detected in prostatic cells obtained by prostatic massage during early diagnosis of prostate cancer (CaP) and discussed their clinical relevance. Blood and first urine voided after prostatic massage were collected in 99 patients with total prostate-specific antigen (PSA) between 4 and 10 ng ml⁻¹, prior to prostate biopsies. Presence of prostatic cells was confirmed by quantitative RT–PCR analysis of PSA mRNA. Genomic DNA was analysed for LOH on six chromosomal regions. One or more allelic deletions were found in prostatic fluid from 57 patients analysed, of whom 33 (58%) had CaP. Sensitivity and specificity of LOH detection and PSA free to total ratio <15% for positive biopsy were respectively 86.7 and 44% (P=0.002) for LOH, and 55 and 74% (P=0.006) for PSA ratio <15%. Analysis of LOH obtained from prostatic tumours revealed similar patterns compared to prostatic fluid cells in 86% of cases, confirming its accuracy. The presence of LOH of urinary prostatic cells obtained after prostatic massage is significantly associated with CaP on biopsy and may potentially help to identify a set of patients who are candidates for further prostate biopsies.

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.

Applicability of biomarkers in the early diagnosis of prostate cancer

Early diagnosis of prostate cancer can increase the curative success rate for this disease. Although serum prostate-specific antigen measurement is regarded as the best conventional tumor marker available, there is little doubt that it has great limitations. The threshold above which biopsies are indicated has now decreased to a serum prostate-specific antigen value of 3 ng/ml, which results in a negative biopsy rate of 70-80%. This can readily be explained by the fact that prostate-specific antigen is not specific for prostate cancer. Clinicians need more sensitive tools to help diagnose prostate cancer and monitor progression of the disease. Molecular oncology is playing an increasing role in the fields of diagnosis and therapy for prostate cancer and has already been instrumental in elucidating many of the basic mechanisms underlying the development and progression of this disease. The identification of new prostate cancer-specific genes, such as DD3PCA3, would represent a considerable advance in the improvement of diagnostic tests for prostate cancer. This could subsequently lead to a reduction of the number of unnecessary biopsies.

uPM3, a new molecular urine test for the detection of prostate cancer

OBJECTIVES

To evaluate, in a multicenter study, the diagnostic performance of a new molecular test uPM3 for detecting prostate cancer cells in urine because of the need for better methods to identify patients at risk of prostate cancer.

METHODS

The uPM3 test is a nucleic acid amplification assay detecting simultaneously in the urine the relative expression of prostate-specific antigen (PSA) mRNA as a marker of prostate cells and PCA3RNA, which is selectively expressed in most types of prostate cancer. The test is performed using the isothermic nucleic acid-based amplification method, and the two targets are simultaneously detected in real-time fluorescence using specific beacons as probes in a thermostated spectrofluorometer. The test was performed on the first voided urine obtained after careful digital rectal examination of the prostate in men undergoing transrectal ultrasound-guided prostate biopsy.

RESULTS

Of 517 patients undergoing biopsy at five centers, 443 (86%) had an assessable sample. Of those, 21%, 55%, and 24% had a total PSA level of less than 4 ng/mL, between 4 and 10 ng/mL, and greater than 10 ng/mL. The corresponding percentage of biopsies positive for cancer in these three groups was 20%, 35%, and 44%. The overall uPM3 sensitivity and specificity was 66% and 89%, respectively. In men with a PSA level less than 4 ng/mL, the sensitivity was 74% and specificity 91%. In those with a PSA level of 4 to 10 ng/mL, the sensitivity was 58% and specificity 91%. In those with a PSA level greater than 10 ng/mL, the sensitivity and specificity was 79% and 80%, respectively. The positive predictive value of uPM3 was 75% compared with 38% for total PSA, and the negative predictive value was 84% compared with 89% and 80% for a PSA cutoff of 2.5 and 4.0 ng/mL, respectively. The overall accuracy was 81% compared with 43% and 47% for total PSA at a cutoff of 2.5 and 4.0 ng/mL, respectively.

CONCLUSIONS

These results suggest that the uPM3 molecular urine test may be an important adjunct to current methods for the detection of early prostate cancer.

D-PCa-2: a novel transcript highly overexpressed in human prostate and prostate cancer

Identification of genes selectively expressed in tumors or individual tissues is a crucial prerequisite for molecular diagnosis and treatment of cancer by addressing molecular targets. By screening an expression database, we identified the novel gene D-PCa-2 (Dresden prostate carcinoma 2), which is highly overexpressed in normal prostate tissue and prostate carcinoma (PCa). The corresponding transcript contained an open reading frame of 453 nucleotides encoding a putative protein of 150 amino acids. A large part of exon 8 of the D-PCa-2 gene shows strong similarity to the high-mobility-group nucleosomal binding protein 2 (HMGN2) cDNA. The highly specific transcription of the D-PCa-2 gene in normal and malignant prostate tissues and in a few additional tumors was demonstrated by using multiple tissue dot blot, cancer profiling dot blot and real-time PCR analyses. Examination of 18 pairs of tumorous and nontumorous prostate tissues from PCa patients by quantitative RT-PCR revealed D-PCa-2 transcripts in all specimens. The potential usefulness of D-PCa-2 as a sensitive marker for metastatic prostate carcinoma cells in lymph nodes was demonstrated by the detection of one LNCaP cell in 1 x 10(5) normal lymph node cells using real-time RT-PCR. Examination of 22 lymph nodes from PCa patients either containing metastatic prostate cancer cells or diagnosed as cancer-free was in full concordance with histopathologic diagnoses. These results validate D-PCa-2 as a transcript with high tissue specificity and with a potential application in the diagnosis of PCa.

Genes differentially expressed in prostate cancer

Because of the heterogeneity of prostate cancer knowledge about the genes involved in prostate carcinogenesis is still very limited. Previously, the use of novel high-throughput technologies offered the possibility to investigate broad gene expression profiles and thus helped to improve understanding of the molecular basis of prostate disease. Many candidate genes have been identified so far which have a more or less strong effect on prostate cancer. This vast number of gene expression changes show that it is unlikely that only one gene promotes prostate cancer. Conversely, it seems more likely that a broad network of molecular changes is involved in the complex cascade of events which lead to tumour formation and progression, respectively. A few of these novel molecular targets are currently under clinical evaluation. This paper gives an overview of several interesting candidate genes which may be useful as improved biomarkers for diagnosis or as targets for developing novel treatment methods.