We evaluated candidate biomarkers of this pathway to predict for pharmacodynamic response to Sunitinib malate. In addition, a 7 ml plasma sample was collected at baseline and again at 4 weeks on all patients to assess possible biomarkers of response. Reported is the mean percent change in plasma concentration for each marker between 4 weeks and baseline.

We will perform immunohistochemistry staining on snap frozen specimens for endothelial and pericyte cell staining as previously described (42). Frozen prostate tumor biopsies are sectioned at 6μm thickness and fixed with acetone for 10 minutes. Endogenous peroxidase activity is quenched with 3% hydrogen peroxide for 15 min and then blocked with 5% normal serum. The slides are incubated with the primary antibody (1;100) overnight at 4 C°, and washed with PBS. Negative controls will be included by omission of the primary antibody. Biotinylated donkey antimouse antibody (1:1000, v/v) will be applied for 30 min at room temperature, followed by application of ABC kit (Vector Lab, Inc., Burlingame, USA). Slides are again washed in PBS and the color is developed by 5 min incubation with diaminobenzidine (DAB) solution. Slides are then counterstained with hematoxylin. Mean protein levels are presented.

Microarray data of 21 specimens from men enrolled who have undergone a prostatectomy and study treatment were compared to data from 21 prostatectomy only specimens. We used previously developed genomic signatures to measure the deregulation of oncogenic pathways built using Bayesian Probit models for 'metagene' factors from a singular value decomposition of top differentially expressed genes. A Monte Carlo Markov Chain was used to generate the predicted probabilities of pathway activity in normalized samples. We predicted the activity of these pathways, leading to the generation of probability measures that have previously reflected the state of pathway activity. These probability scores are interpreted as gene expression values to describe pathway activity patterns. A probability near 0 indicates a low chance of pathway activity; a probability near 1 indicates a higher likelihood of activity. Differences (treatment - control) in mean probability for each pathway are reported.

Measure Interstitial fluid pressure (IFP) pre-treatment and during treatment to indirectly measure the effect of Sunitinib malate on transcapillary transport and correlate with other biologic evidence of treatment effect.Eligible patients who sign consent will undergo a baseline transrectal ultrasound (TRUS)-guided measurement of tumor IFP. Participants will then begin treatment with daily oral Sunitinib malate with biweekly monitoring for response and toxicity. After 4 weeks of therapy, patients undergo a repeat TRUS and tumor IFP measurement. Following a 1 to 2 week wash out period, patients undergo prostatectomy with pathologic tissue collection. This will be performed as a means to evaluate whether Sunitinib malate has the ability to decrease tumor IFP, and whether this correlates with other tr

Adverse events were collected using Common Terminology Criteria for Adverse Events (CTCAE) version 3.0 and were converted to version 4.0 for the purposes of ClinicalTrials.gov reporting.

Pathologic changes will be described using immuno-histochemical techniques (assessment of microvessel density (MVD)) using paraffin-embedded samples and freshly cut slides from the block which are deparaffinized and rehydrated through graded alcohol, where applicable. Antigen retrieval will be accomplished by microwaving in citrate buffer from 5 to 7 minutes for the MVD analysis. Results are reported as the difference in pre and post MVD. Units for MVD are number of CD31 cells per high powered field.

Two patients did not complete surgery, and five patients did not have adequate tissue samples, leaving 23 patients for analysis

We evaluated candidate biomarkers of this pathway to predict for pharmacodynamic response to Sunitinib malate. In addition, a 7 ml plasma sample was collected at baseline and again at 4 weeks on all patients to assess possible biomarkers of response. Reported is the mean percent change in plasma concentration for each marker between 4 weeks and baseline.

17 patients had adequate measurements at both time points, were on an adequate dose, and took treatment at the correct time points.

We will perform immunohistochemistry staining on snap frozen specimens for endothelial and pericyte cell staining as previously described (42). Frozen prostate tumor biopsies are sectioned at 6μm thickness and fixed with acetone for 10 minutes. Endogenous peroxidase activity is quenched with 3% hydrogen peroxide for 15 min and then blocked with 5% normal serum. The slides are incubated with the primary antibody (1;100) overnight at 4 C°, and washed with PBS. Negative controls will be included by omission of the primary antibody. Biotinylated donkey antimouse antibody (1:1000, v/v) will be applied for 30 min at room temperature, followed by application of ABC kit (Vector Lab, Inc., Burlingame, USA). Slides are again washed in PBS and the color is developed by 5 min incubation with diaminobenzidine (DAB) solution. Slides are then counterstained with hematoxylin. Mean protein levels are presented.

Due to changes in the field, this test was not performed due to lack of relevance.

Microarray data of 21 specimens from men enrolled who have undergone a prostatectomy and study treatment were compared to data from 21 prostatectomy only specimens. We used previously developed genomic signatures to measure the deregulation of oncogenic pathways built using Bayesian Probit models for 'metagene' factors from a singular value decomposition of top differentially expressed genes. A Monte Carlo Markov Chain was used to generate the predicted probabilities of pathway activity in normalized samples. We predicted the activity of these pathways, leading to the generation of probability measures that have previously reflected the state of pathway activity. These probability scores are interpreted as gene expression values to describe pathway activity patterns. A probability near 0 indicates a low chance of pathway activity; a probability near 1 indicates a higher likelihood of activity. Differences (treatment - control) in mean probability for each pathway are reported.

21 patients had adequate samples for analysis.

Measure Interstitial fluid pressure (IFP) pre-treatment and during treatment to indirectly measure the effect of Sunitinib malate on transcapillary transport and correlate with other biologic evidence of treatment effect.Eligible patients who sign consent will undergo a baseline transrectal ultrasound (TRUS)-guided measurement of tumor IFP. Participants will then begin treatment with daily oral Sunitinib malate with biweekly monitoring for response and toxicity. After 4 weeks of therapy, patients undergo a repeat TRUS and tumor IFP measurement. Following a 1 to 2 week wash out period, patients undergo prostatectomy with pathologic tissue collection. This will be performed as a means to evaluate whether Sunitinib malate has the ability to decrease tumor IFP, and whether this correlates with other tr

This was an optional test and no patients chose to participate.

Pathologic changes will be described using immuno-histochemical techniques (assessment of apoptotic/proliferative indices and microvessel density (MVD)) using paraffin-embedded samples and freshly cut slides from the block which are deparaffinized and rehydrated through graded alcohol, where applicable. Antigen retrieval will be accomplished by microwaving in citrate buffer from 5 to 7 minutes for the Ki-67 and MVD analysis. Mean difference in %proliferation (Ki67 positive nuclei out of total nuclei) between pre and post treatment will be reported.

Two patients did not complete surgery, and five patients did not have adequate tissue samples, leaving 23 patients for analysis