Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.

Integration of ERG gene mapping and gene-expression profiling identifies distinct categories of human prostate cancer.

OBJECTIVE: To integrate the mapping of ERG alterations with the collection of expression microarray (EMA) data, as previous EMA analyses have failed to consider the genetic heterogeneity and complex patterns of ERG alteration frequently found in cancerous prostates. MATERIALS AND METHODS: We determined genome-wide expression levels with GeneChip Human Exon 1.0 ST arrays (Affymetrix, Santa Clara, CA, USA) using RNA prepared from 35 specimens of prostate cancer from 28 prostates. RESULTS: The expression profiles showed clustering, in unsupervised hierarchical analyses, into two distinct prostate cancer categories, with one group strongly associated with indicators of poor clinical outcome. The two categories are not tightly linked to ERG status. By analysis of the data we identified a subgroup of cancers lacking ERG rearrangements that showed an outlier pattern of SPINK1 mRNA expression. There was a major distinction between ERG rearranged and non-rearranged cancers that involves the levels of expression of genes linked to exposure to beta-oestradiol, and to retinoic acid. CONCLUSIONS: Expression profiling of prostate cancer samples containing single patterns of ERG alterations can provide novel insights into the mechanism of prostate cancer development, and support the view that factors other than ERG status are the major determinants of poor clinical outcome.

Detection of TMPRSS2-ERG translocations in human prostate cancer by expression profiling using GeneChip Human Exon 1.0 ST arrays.

Translocation of TMPRSS2 to the ERG gene, found in a high proportion of human prostate cancer, results in overexpression of the 3'-ERG sequences joined to the 5'-TMPRSS2 promoter. The studies presented here were designed to test the ability of expression analysis on GeneChip Human Exon 1.0 ST arrays to detect 5'-TMPRSS2-ERG-3' hybrid transcripts encoded by this translocation. Monitoring the relative expression of each ERG exon revealed altered transcription of the ERG gene in 15 of a series of 27 prostate cancer samples. In all cases, exons 4 to 11 exhibited enhanced expression compared with exons 2 and 3. This pattern of expression indicated that the most abundant hybrid transcripts involve fusions to ERG exon 4, and RT-PCR analyses confirmed the joining of TMPRSS2 exon 1 to ERG exon 4 in all 15 cases. The exon expression patterns also indicated that TMPRSS2-ERG fusion transcripts commonly contain deletion of ERG exon 8. Analysis of gene-level data from the arrays allowed the identification of genes whose expression levels significantly correlated with the presence of the translocation. These studies demonstrate that expression analyses using exon arrays represent a valuable approach for detecting ETS gene translocation in prostate cancer, in parallel with analyses of gene expression profiles.

Visually directed high-intensity focused ultrasound for organ-confined prostate cancer: A proposed standard for the conduct of therapy.

OBJECTIVE: To propose a standard for the conduct of visually directed transrectal high-intensity focused ultrasound (HIFU) and to offer a formal description of the changes observed on B-mode ultrasonography (US) during this procedure. We describe our early experience of using two different treatment methods; algorithm-based HIFU and visually directed HIFU for the treatment of organ-confined prostate cancer. PATIENTS AND METHODS: Between November 2004 and October 2005, 34 men were treated using the Sonablate-500 (Focus Surgery, Indianapolis, IN, USA) as primary therapy for T1 or T2 prostate cancer. None had had previous hormone therapy and all had > or = 3-month PSA nadirs recorded at the follow-up. Nine men were treated using an algorithm-based protocol (group 1) and 25 using visually directed therapy (group 2). The conduct of visually directed treatment was described and changes seen using B-mode US were categorized using three 'Uchida' grades. RESULTS The mean PSA nadir achieved in group 2 was 0.15 ng/mL, vs 1.51 ng/mL in group 1 (P < 0.005). In group 2, 21 of 25 men achieved PSA nadirs of < or = 0.2 ng/mL 3 months after treatment. Seven men achieved undetectable PSA values. The occurrence rate of treatment-related toxicity was similar in both groups. CONCLUSION: Visually directed, transrectal HIFU enables clinically important and statistically significantly lower PSA nadirs to be achieved than algorithm-based HIFU. This is the first reported experience of visually directed HIFU for the treatment of organ-confined prostate cancer. We think that this is the first attempt to standardize the conduct of therapy; such standardization facilitates teaching it, and makes it possible to derive quality standards. The standardization of the conduct of therapy is a key step in the process of health technology assessment.

Urine dendritic cells: a noninvasive probe for immune activity in bladder cancer?

OBJECTIVES: To test the hypothesis that dendritic cells (DC), antigen-presenting cells with the potential to stimulate primary T-cell responses, may appear in the urine of patients with bladder cancer, and that their characteristics may reflect those of DC in cancer tissue. PATIENTS AND METHODS: Cells from digested tissue of transurethral resection specimens from eight patients and urine from 18 with bladder cancers were analysed using flow cytometry, immunohistochemistry and electron microscopy. Urine samples from 12 patients were also analysed during intravesical bacillus Calmette-Guerin (BCG) therapy. RESULTS: Immature DC positive for major histocompatibility complex class II antigens, negative for markers of other leukocyte lineages and with low levels of co-stimulatory markers, were identified in CD45-positive cells isolated immediately from cancer tissue or amongst cells migrating from tissue fragments after overnight culture. Immature-phenotype DC were also identified in the urine of patients with bladder cancer. Their identity was confirmed by immunohistochemistry and electron microscopy. Using these methods, DC were monitored from the bladder during BCG installation for bladder cancer in 12 patients for a mean of 10 months. Of six patients who developed a recurrence of their bladder cancer over this period, all but one showed a lower percentage of DC in their urine at the end of their initial treatment. CONCLUSION: We identified DC in the urine of patients with bladder cancer for the first time. We speculate that variability in the percentage of urinary DC may reflect changes in immunological activity at the tumour site; prospective studies are required to evaluate the relevance of these DC counts and characteristics to clinical outcome.