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Objectives: To identify an appropriate reference gene for the analysis of circulating micro-ribonucleic acid in patients with urological malignancies. Methods: Serum from patients with prostate cancer ( n = 24), bladder cancer ( n = 24), renal cell carcinoma ( n = 24) and control subjects ( n = 48) was spiked with cel-miR-39, and then ribonucleic acid was isolated. Quantitative real-time polymerase chain reaction was used to determine the levels of candidate reference genes ( RNU1-4, RNU6-2, SNORD43, SNORD44, SNORD48, S NORA74A, miR-let-7a-1, miR-106a). Reference gene stability was determined using the NormFinder, geNorm and comparative delta-Ct algorithm. The effect of normalization was tested with miR-21 as the target gene, as this was previously suggested to be upregulated in cancer patients' serum. Results: Recovery of cel-miR-39 (mean 11.6%, range 1-56%) was similar in control subjects and cancer patients. SNORD44 and SNORD74A levels were around the detection limit of the assay and were thus omitted. All remaining candidates showed satisfying stability; SNORD43 was the most stable reference gene using all three algorithms. A combination of two genes ( SNORD43, RNU1-4) increases the stability somewhat. The level of miR-21 was similar in cancer patients and healthy controls, irrespective of the normalization strategy. Conclusions: SNORD43 is a suitable reference gene for the analysis of circulating micro-ribonucleic acid in patients with urological malignancies. Our study questions the suitability of miR-21 as a biomarker for uro-oncological patients. [ABSTRACT FROM AUTHOR]

Global histone modification patterns have been shown to be a predictive factor of recurrence in various cancers. We analyzed global histone-3-lysine-27 (H3K27) methylation in prostate cancer (PCA) tissues. H3K27 mono-, di-, and tri-methylation patterns were different in nonmalignant prostate tissue, localized PCA, metastatic PCA, and castration-resistant PCA. H3K27 mono-methylation was correlated with pT-stage, capsular penetration, seminal vesicle infiltration, and Gleason score in localized PCA and may therefore indicate adverse prognosis. [ABSTRACT FROM AUTHOR]

OBJECTIVE To investigate the role of circulating mitochondrial DNA (mtDNA) in patients with localized prostate cancer, as recent reports show that patients with advanced cancer have increased levels of mtDNA. PATIENTS AND METHODS DNA was isolated from the serum of 100 patients with prostate cancer and 18 with benign prostate hyperplasia (BPH). A quantitative real-time polymerase chain reaction was used to amplify 79 bp and 230 bp fragments of the mitochondrial 16s-RNA gene, the short fragment representing total mtDNA, including mtDNA truncated by apoptosis, and the long fragment representing mostly mtDNA from other cell death entities. mtDNA integrity was defined as the ratio of long to short mtDNA fragments. RESULTS The short and long mtDNA levels, and mtDNA integrity, were similar in patients with BPH and cancer ( P = 0.940, 0.211 and 0.441, respectively), and were not correlated with clinical or pathological variables, e.g. age, prostate-specific antigen (PSA) level, cT stage, pT stage, seminal vesicle infiltration, lymph node invasion, or Gleason score ( P = 0.075 to 0.961). However, patients with high levels of short mtDNA (>75th percentile) had a greater risk of PSA progression and this variable was the strongest predictor of PSA recurrence in a multivariate Cox analysis ( P = 0.023; hazard ratio 0.31; 95% confidence interval 0.113–0.851). CONCLUSION Circulating mtDNA levels did not distinguish between patients with prostate cancer or BPH. However, there was a significant increase in short mtDNA fragments in patients with early PSA recurrence after radical prostatectomy. [ABSTRACT FROM AUTHOR]

Gene silencing by promoter DNA hypermethylation is common in PCA. The role of HXKy methylation as an up-/downstream or parallel silencing mechanism is not yet clear. We analyzed HXKy methylation at gene sites that are aberrantly DNA-methylated in PCA (i.e. GSTP1, RARβ, APC and PTGS2). Cancerous (PC3, DU145, LNCaP) and benign prostate hyperplasia (BPH1) cell lines were studied using chromatin immunoprecipitation and methylation specific PCR. Gene expression was analyzed using quantitative RT-PCR. In PCA, histone modifications characteristic of gene repression (di-/tri-methylated H3K9, H3K27, H4K20) were predominantly observed at the studied gene sites and paralleled aberrant DNA hypermethylation. In BPH, no aberrant DNA hypermethylation and mostly histone modifications supporting active gene expression (H3K4, H3K79 di-/tri methylation) were seen at the respective gene sites. Mono-methylated H3K4 and H3K9 modifications that have moderate effects on gene expression were frequent in both PCA and BPH. PC3 cells grown in the presence of the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (aza) resulted in DNA demethylation and moderate gene reexpression whereas repressive HXKy di-methylation increased 1.5-3 fold and tri-methylation was mostly unchanged. Removal of aza reverses gene expression. These findings suggest that HXKy methylation is upstream to DNA hypermethylation in PCA. [ABSTRACT FROM AUTHOR]

Cancer patients have increased levels of serum DNA fragments (SDF) compared to most patients with non-malignant disease and healthy individuals. In PCA, DNA hypermethylation is also frequently observed (>80%) at promoter CpG islands of GSTP1, PTGS2 and TIG1. Therefore we analysed hypermethylation of these genes in SDF from patients with PCA (n=168) and benign prostate hyperplasia (BPH; n=42) and controls (n=11) for information about the cellular origin of DNA. SDF concentrations and the hypermethylated fractions were analysed using a methylation-sensitive restriction enzyme based real-time PCR. SDF levels were significantly increased in PCA vs BPH vs controls (65 vs 20 vs 7 ng/mL; p<0.001). Hypermethylation of GSTP1, TIG1 or PTGS2 was more frequently detected in PCA than in BPH patients and controls (overall 47% vs 8% vs 0%; p<0.001), but did not exceed 10% of total DNA. SDF levels distinguished PCA from BPH patients with a sensitivity of 83% and specificity of 69%. The diagnostic significance of SDF was greater than that of hypermethylation data. In conjunction with SDF, hypermethylation numbers did not contribute any further information. Both SDF levels and the hypermethylation status were not correlated to advanced tumor stage or grade (p>0.05). In summary SDF is a promising diagnostic marker in PCA. It does not primarily originate from tumor cells but from apoptotic and necrotic cells surrounding the tumor. [ABSTRACT FROM AUTHOR]

Abstract: Objective: Cell-free circulating mitochondrial DNA (mtDNA) has been proposed as universal diagnostic and prognostic biomarker in cancer patients. Patients and methods: Cell-free DNA was isolated from 1 ml serum from patients with bladder cancer (BCA, n = 84), renal cell carcinoma (RCC, n = 33), and prostate cancer (CaP, n = 23), and compared with healthy individuals (n = 79). Quantitative real-time PCR was used to analyze the levels of a 79 bp (mtDNA-79), and 220 bp (mtDNA-220) fragment of the mitochondrial specific 16S-RNA. The mitochondrial DNA integrity (mtDNA-integrity) was defined as ratio of mtDNA-220 to mtDNA-79 fragments. Results: In healthy controls, mtDNA-79 levels were increased in male volunteers; mtDNA-230 levels and mtDNA-integrity were correlated with age. Neither mtDNA levels nor mtDNA-integrity were correlated with age or gender in cancer patients. Circulating mtDNA-79 (median 8.75 × 106 vs. 0.43 × 106 copies/ml) and mtDNA-230 (8.11 × 106 vs. 0.27 × 106 copies/ml) levels were significantly increased in cancer patients and allowed sensitive (84%) and specific (97%) discrimination from healthy controls. mtDNA levels were unequally distributed among the different cancer entities (mtDNA-79: BCA 9.54 × 106 vs. RCC 6.69 × 106 vs. CaP 4.48 × 106 copies/ml; mtDNA-230: BCA 9.78 × 106 vs. RCC 6.74 × 106 vs. CaP 1.94 × 106 copies/ml). The mtDNA-integrity was increased in RCC and BCA patients compared to control subjects and CaP patients. Serum mtDNA-integrity was correlated with pathological stage in RCC and with tumor grade in BCA patients. Conclusion: Circulating mtDNA levels are associated with gender and age in healthy individuals, but not in cancer patients. Quantification of circulating mtDNA may help identify patients with urologic malignancies. [Copyright &y& Elsevier]

Abstract: Gene silencing by epigenetic mechanisms is frequent in prostate cancer (PCA). The link between DNA hypermethylation and histone modifications is not completely understood. We chose the GSTP1 gene which is silenced by hypermethylation to analyze the effect of the histone deacetylase inhibitor depsipeptide on DNA methylation and histone modifications at the GSTP1 promoter site. Prostate cell lines (PC-3, LNCaP, and BPH-1) were treated with depsipeptide; apoptosis (FACS analysis), GSTP1 mRNA levels (quantitative real-time PCR), DNA hypermethylation (methylation-specific PCR), and histone modifications (chromatin immunoprecipitation) were studied. Depsipeptide induced apoptosis in PCA cells, but not a cell cycle arrest. Depispeptide reversed DNA hypermethylation and repressive histone modifications (reduction of H3K9me2/3 and H3K27me2/3; increase of H3K18Ac), thereby inducing GSTP1 mRNA re-expression. Successful therapy requires both, DNA demethylation and activating histone modifications, to induce complete gene expression of epigenetically silenced genes and depsipeptide fulfils both criteria. [Copyright &y& Elsevier]

Abstract: The presence of small amounts of circulating DNA in plasma was demonstrated 60 years ago. Since then, cell-free DNA has been tested for quantity, fragmentation pattern, and tumor-specific sequences in patients with various malignancies. Recent studies have shown that cell-free DNA levels are distinctly increased in most patients with prostate cancer (PCA) and that the DNA fragmentation pattern is different from healthy individuals and patients with benign prostate disease. The origin of this circulating DNA remains largely unknown, but it is established that a small fraction of the DNA is derived from the tumor itself, and genetic (allelic imbalances) and epigenetic (DNA methylation) alterations are regularly detected in patients with PCA. The detection of increased DNA levels and tumor-specific DNA sequences may provide diagnostic and prognostic information. The recent findings in the emerging field of cell-free DNA will be discussed. [Copyright &y& Elsevier]

Abstract Background Global histone modifications have been implicated in the progression of various tumour entities. Our study was designed to assess global methylation levels of histone 4 lysine 20 (H4K20me1-3) at different stages of prostate cancer (PCA) carcinogenesis. Methods Global H4K20 methylation levels were evaluated using a tissue microarray in patients with clinically localized PCA (n = 113), non-malignant prostate disease (n = 27), metastatic hormone-naive PCA (mPCA, n = 30) and castration-resistant PCA (CRPC, n = 34). Immunohistochemistry was performed to assess global levels of H4K20 methylation levels. Results Similar proportions of the normal, PCA, and mPCA prostate tissues showed strong H4K20me3 staining. CRPC tissue analysis showed the weakest immunostaining levels of H4K20me1 and H4K20me2, compared to other prostate tissues. H4K20me2 methylation levels indicated significant differences in examined tissues except for normal prostate versus PCA tissue. H4K20me1 differentiates CRPC from other prostate tissues. H4K20me1 was significantly correlated with lymph node metastases, and H4K20me2 showed a significant correlation with the Gleason score. However, H4K20 methylation levels failed to predict PSA recurrence after radical prostatectomy. Conclusions H4K20 methylation levels constitute valuable markers for the dynamic process of prostate cancer carcinogenesis.

Objectives: To analyze circulating microRNAs (miRNA) in serum as non-invasive biomarker in patients with localized prostate cancer (PCA), benign prostate hyperplasia (BPH) and healthy individuals (HI). Methods: Total RNA was isolated from serum samples and the circulating levels of different RNA species (miRNA, miR-16; small nuclear RNA, RNU1A-1; messenger RNA, HPRT1), as well as of 4 oncogenic miRNAs (miR-26a, miR-32, miR-195, miR-let7i), were determined using a quantitative real-time polymerase chain reaction. We also evaluated miRNA levels in a second cohort of 10 PCA patients in cancer/nonmalignant tissue, and pre- and post-prostatectomy serum samples. Results: The levels of miR-16 and RNU1A-1were reliably measured, whereas HPRT1 levels were often below the detection limit of our assay. Circulating oncogenic miRNA levels were different, and especially the miR-26a level allowed sensitive (89%) discrimination of PCA and BPH patients at a moderate specificity (56%; area under the curve [AUC]: 0.703); the analysis of oncogenic miRNAs in combination increased the diagnostic accuracy (sensitivity: 78.4%; specificity: 66.7%; AUC: 0.758). Despite the low number of patients limiting the statistical power of the study, we observed correlations with clinical-pathologic parameters: miR-16, miR-195, and miR-26a were significantly correlated with surgical margin positivity; miR-195 and miR-let7i were significantly correlated with the Gleason score. Tissue miRNA levels were correlated with preprostatectomy miRNA levels in serum, and serum miRNA decreased after prostatectomy, thereby indicating tumor-associated release of miRNA. Conclusions: Tumor-associated miRNAs in serum allow noninvasive discrimination of PCA and BPH. [ABSTRACT FROM AUTHOR]