Karnes, R. Jeffrey

Abstract Gleason score 7 (GS7) prostate cancer [tumors with both Gleason patterns 3 (GP3) and 4 (GP4)] portends a significantly more aggressive tumor than Gleason score 6 (GS6). It is, therefore, critical to understand the molecular relationship of adjacent GP3 and GP4 tumor cell populations and relate molecular abnormalities to disease progression. To decipher molecular relatedness, we used laser capture microdissection (LCM) and whole-genome amplification (WGA) to separately collect and amplify DNA from adjacent GP3 and GP4 cell populations from 14 cases of GS7 prostate cancer. We then carried out massively parallel mate-pair next generation sequencing (NGS) to examine the landscape of large chromosomal alterations. We identified four to 115 DNA breakpoints in GP3 and 17 to 480 in GP4. Our findings indicate that while GP3 and GP4 from the same tumor each possess unique breakpoints, they also share identical ones, indicating a common origin. Approximately 300 chromosomal breakpoints were localized to the regions affected in at least two tumors, whereas more than 3,000 were unique within the set of 14 tumors. TMPRSS2–ERG was the most recurrent rearrangement present in eight cases, in both GP3 and GP4. PTEN rearrangements were found in five of eight TMPRSS2–ERG fusion–positive cases in both GP3 and GP4. Hierarchical clustering analysis revealed that GP3 has greater breakpoint similarity to its partner GP4 compared with GP3 from different patients. We show evidence that LCM, WGA, and NGS of adjacent tumor regions provide an important tool in deciphering lineage relationships and discovering chromosomal alterations associated with tumor progression. Cancer Res; 73(11); 3275–84. ©2013 AACR.

Abstract Introduction: Multivariable models that predict biochemical recurrence (BCR) can indicate patients at higher risk for developing clinical progression after prostatectomy. However, most patients that experience BCR do not metastasize or die from prostate cancer, making BCR an unreliable surrogate endpoint. In this study we compared the clinical and genomic characteristics of prostatectomy patients in order to better delineate the relationship between BCR and aggressive prostate cancer. Methods: Postoperative patients were retrospectively classified into three outcome groups: NED (no evidence of disease recurrence); BCR-only (patients that experienced BCR but didn't have progressive disease as evidenced by bone or CT scans); and CP (clinical progression with BCR plus positive CT or bone scans). Patient specimens were from the Mayo Clinic Radical Prostatectomy Registry, selected using a nested case-control design with 14 years median follow-up. RNA expression levels from FFPE tumor specimens were measured with 1.4 million feature whole-transcriptome oligonucleotide microarrays on 106 matching patients from each outcome group (total 318 patients). We analyzed the clinical covariates of the outcome groups in a pairwise manner (NED vs. BCR-only; NED vs. CP; CP vs. BCR-only), using a conditional logistic model in univariable and multivariable analyses. We performed feature reduction for the genomic data set using Kruskal-Wallis tests and regularized logistic regression. Principal Component Analysis (PCA) was used to quantify the variance of the genomic data with respect to the patient outcome groups. Results: Our initial hypothesis was that all three outcome groups would have different clinical and genomic characteristics. Univariable analysis of clinical variables failed to show statistically significant differences between NED and BCR-only groups. Multivariable analysis of the clinical variables also failed to show statistically significant differences between NED and BCR-only groups. Among the clinical variables only pathological Gleason score was statistically significant when comparing the BCR-only vs. CP and NED vs. CP groups. Genomic analysis found 363 coding and non-coding features that passed thresholds for differential expression between the three outcome groups. PCA established that the primary source of variance in the genomic data stemmed from the separation of CP from NED and BCR-only patients; whereas only a small amount of variance separates NED and BCR-only groups. The 363 features were further compared in the three outcome groups using Wilcoxon tests, adjusting for false-discovery using Benjamini-Hochberg. At a cutoff of p < 0.001 there were no features differentially expressed between NED and BCR-only, while 52 and 34 statistically significant features were found in the NED vs. CP and CP vs. BCR-only comparisons, respectively. Conclusion: Considering the clinical and genomic results together, we find that: 1) Patients that developed clinical progression were significantly different from those that did not, irrespective of whether they experienced BCR or not; 2) the NED and BCR-only groups were statistically very similar to each other. We therefore conclude that BCR may not be the most appropriate endpoint for predictive models that attempt to stratify patients at risk for progression. This abstract is also presented as Poster B44. Citation Format: Anamaria Crisan, Elai Davicion, R. Jeffery Karnes, Robert B. Jenkins, Mercedeh H. Ghadessi, Christine Buerki, Eric J. Bergstrahl, Nicholas Erho, Ismael A. Vergara, Karla V. Ballman, Peter C. Black, Timothy J. Triche. Biochemical recurrence is not a definitive surrogate endpoint for development of clinically useful predictive models for post-prostatectomy patients [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr PR4.

Abstract Tumor-associated hypoxia has been associated with malignant progression, metastasis and resistance to therapy. We studied the role of oxygen tension (pO2) in modulating the properties of cultured human prostate cancer (CaP) cells. In air, where oxygen tension (pO2) is approximately 20 kPa, cultured CaP cells expressed lower levels of transcripts associated with cancer and urologic disease; reducing pO2 to 2 kPa made these levels comparable to those in surgical CaP specimens suggesting that hypoxically cultured cells, rather than normoxically cultured cells, express genes at levels akin to those in tumor cells in situ. In human primary CaP tissue, transcripts of hypoxia-associated genes DLG7, CCNB1 and HMMR were overexpressed and associated with Gleason score and disease prognosis; this implies the potential prognostic value of these transcripts. While hypoxia affected the CaP cell proteome mostly quantitatively, it did affect expression of tumor–associated antigens and suggested the potential therapeutic relevance of the hypoxic antigenic landscape. Overall, our results suggest that hypoxia modifies cellular properties of cultured CaP cells towards a phenotype more similar to tumor cells in situ. Introduction of pO2 as a variable can constitute a tool for the identification of more effective prognostic biomarkers and development of better therapy for CaP and, possibly, other tumors. Citation Format: Christian R. Gomez, Stanimir Vuk-Pavlovic, Farhad Kosari, Jan Marie Munz, Claire Schreiber, Gaylord Knutson, Cristine Charlesworth, R. Jeffrey Karnes, John Cheville, George Vasmatzis. Prognostic value of hypoxia-associated genes in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr C43.

What's known on the subject? and What does the study add? Variations in the type of urinary diversion exist for patients undergoing radical cystectomy. Although its use has been increasing from 2001 to 2008, patients who are older, female, and primary insured by Medicaid are less likely to receive continent diversions. Furthermore, patients treated surgically at high‐volume and teaching hospitals are more likely to receive continent diversions. Objective To describe the contemporary trends in urinary diversion among patients undergoing radical cystectomy ( RC ) for bladder cancer; and elucidate whether socioeconomic disparities persist in the type of diversion performed in the USA from a population‐based cohort. Patients and Methods Using the Nationwide Inpatient Sample, we identified patients who underwent RC for bladder cancer between 2001 and 2008. Multivariable regression models were used to identify patient and hospital covariates associated with continent urinary diversion and enumerate predicted probabilities for statistically significant variables over time. Results Overall, 55 635 (92%) patients undergoing RC for bladder cancer received incontinent urinary diversion, while 4552 (8%) patients received continent diversion from 2001 to 2008. Receipt of continent urinary diversion increased from 6.6% in 2001–2002 to 9.4% in 2007–2008 ( P < 0.001 for trend). Patients who were older (odds ratio [ OR ] 0.93; P < 0.001), female ( OR 0.52; P < 0.001) and insured by Medicaid ( OR 0.54; P = 0.002) were less likely to receive continent urinary diversion. However, patients treated at teaching ( OR 2.14; P < 0.001) and high‐volume hospitals ( OR 2.39; P = 0.04) had higher odds of continent urinary diversion. Predicted probabilities of continent diversion remained lower for female patients, Medicaid insurance status, and non‐teaching and medium/low‐volume hospitals over time. Conclusions In this nationally representative sample of hospitals from 2001 to 2008, the use of continent diversion in RC gradually increased. Although variations in urinary diversion exist by hospital teaching status, case volume, patient gender and primary health insurance, increased attention in expanding the use of continent diversions may help reduce these disparities for patients undergoing RC for bladder cancer.

ObjectivesTo examine the ability of standard and saturation transrectal prostate biopsy techniques to predict appropriate candidates for active surveillance.MethodsBetween 2005 and 2007, 500 consecutive patients underwent transrectal ultrasound‐guided biopsy by a standard template (12 cores) or saturation template (≥18 cores, median 27 cores), with subsequent radical prostatectomy. Using the criteria of Gleason score ≤6, clinical stage T1 or T2a, prostate‐specific antigen <10 and ≤33% of cores involved, 218 patients were potential candidates for active surveillance. Pathology results from the prostatectomy specimens were used to determine the accuracy of each biopsy technique. Biochemical failure after prostatectomy was evaluated using logistic and Cox proportional hazards regression.ResultsA standard biopsy was carried out for 124 patients and saturation biopsy for 94 patients. There was no statistically significant difference between the groups in terms of median age (P = 0.14), preoperative prostate‐specific antigen (P = 0.52) and clinical stage (P = 0.23). Similar rates of Gleason score ≥7 at the time of radical prostatectomy were found, with 14% for standard biopsy and 15% for saturation biopsy (P = 0.70). Upstaging was shown in two standard biopsy patients (1.6%) and no saturation biopsy patients (P = 0.62). A multivariate analysis adjusting for prior prostate biopsy, preoperative prostate‐specific antigen and clinical stage showed no difference in the rate of upgrading based on biopsy technique (P = 0.26). During follow up, 5‐year biochemical failure‐free survival estimates were not significantly different (P = 0.11).ConclusionsIn men with prostate cancer, standard and saturation transrectal prostate biopsies techniques are equally predictive of candidates for active surveillance.

BackgroundTo evaluate the impact of adjuvant hormonal therapy after radical prostatectomy on overall survival in high‐risk prostate cancer patients, stratified by comorbidity status.MethodsWe identified 1247 patients who underwent radical prostatectomy from 1988 to 2004 for high‐risk prostate cancer, as defined by National Comprehensive Cancer Network classification. Comorbidity status was stratified by Charlson Comorbidity Index as 0, 1 or >2, as well as by the presence or absence of cardiovascular disease. Overall survival was estimated by the Kaplan–Meier method, and compared within each comorbidity category/adjuvant hormonal therapy strata with the log–rank test.ResultsMedian patient age was 65 years, and the median postoperative follow up was 11.2 years. In total, 419 patients (34%) received adjuvant hormonal therapy. The distribution of Charlson Comorbidity Index was 0, 1 and ≥2 in 861 (69%), 244 (20%) and 142 (11%) patients, respectively. The 10‐year overall survival for patients who received adjuvant hormonal therapy versus those who did not was 75% versus 82% (P = 0.54) for patients with Charlson Comorbidity Index = 0, 72% versus 76% (P = 0.83) with Charlson Comorbidity Index = 1, and 70% versus 68% (P = 0.33) with Charlson Comorbidity Index ≥2. Meanwhile, 155 (12%) patients had cardiovascular disease, and the 10‐year overall survival for patients with cardiovascular disease who received adjuvant hormonal therapy was 72%, compared with 76% without adjuvant hormonal therapy (P = 0.97). On multivariate analysis, receipt of adjuvant hormonal therapy was not associated with non‐prostate cancer mortality (P = 0.24).ConclusionsAdjuvant hormonal therapy after radical prostatectomy for high‐risk prostate cancer does not increase non‐prostate cancer mortality, even among patients with multiple comorbidities. Additional studies are warranted to determine optimal multimodal treatment approach for high‐risk patients.