Abstract B31: Establishing the use of genomic profiling on rare prostate cancer disseminated tumor cells
Authors: Schoenborn Jamie R. , Xia Jing , Larson Sandy , Brown Lisha , Morrissey Colm , Lange Paul , Nelson Peter S. , Vessella Robert L. , Fang Min 
Published: May 2013

Abstract
Objective: Dissemination of prostate cancer tumor cells remains a critical challenge in understanding disease progression and effective long-term treatment of patients. Disseminated tumor cells (DTCs) from bone marrow are resistant to chemotherapy and radiation, and represent a potential long-lived source for lethal metastases. Quantification of disseminated and circulating tumor cells provides promise as a novel diagnostic in measuring tumor burden and assessing the risk of relapse. However, very limited knowledge exists about the biology of these rare cells, including the genomic aberrations associated with clinical outcome.
Methods: DTCs are immunomagnetically enriched from bone marrow aspirates, then individually captured under the microscope based on immunofluorescent staining of EpCaM cell surface molecules. We have established use of whole genome amplification and high-density SNP-CGH arrays to genomically profile rare DTC populations (n=2-25 cells). Using Fused Lasso and Nexus Copy Number software, we quantify and characterize copy number alterations and loss-of-heterozygosity regions among samples isolated from 58 patients taken at the time of radical prostectomy and from 13 patients with advanced, metastatic or lethal prostate cancer. We classify DTC aberrations by tumor stage and compare to those aberrations identified in primary and metastatic tumors. Regions of interest are validated using a highly sensitive quantitative real-time PCR assay. In addition, we have completed extensive optimization of analysis parameters to handle the increased probe variation associated with low input DNA quantity and whole genome amplification.
Results: DTCs isolated at the time of radical prostatectomy from early stage prostate cancer patients are generally heterogeneous and are marked with limited focal aberrations. Focal deletions of less than 100 kb are frequent events in these samples, as are focal gains of less than 500 kb, albeit less frequently. While many of these focal copy number changes are identified in regions of common copy number variation (CNV) within the population, a considerable number are rare and unique to DTCs. Cancer-specific alterations are observed in members of the cadherin family and transcription factors SIX3, SOX4, SOX17 and GATA6. Because most abberations are patient-specific, bioinformatic analysis is used to illuminate commonly altered biological pathways. In contrast, DTCs from patients with advanced stages of prostate cancer typically show frequent and large (&gt;1 Mb) clonal amplifications and deletions, suggesting a high degree of genomic instability that is common among these patients. Aberrant regions that are uniquely identified in DTCs from patients with advanced, metastatic and castrationresistant prostate cancers include gain of 1q43–q44 and 1q31.3–q41. In addition, several regions were found to be recurrent among at least 25% of metastatic tumors and DTCs from advanced stages, including in order of prevalence: +8q, −8p, +9q, −13, −22, −16q, −7q, −6q13–q22.31, +3q24–q26.1, +11q13.2–13.4, −17p13.3–p12 and +2p16.3–p16.2.
Conclusions: We have established methods and quality control measures for genome-wide profiling of rare cell populations. These methods will be functionally useful to gain a new understanding of the genomic aberrations that drive DTC dissemination, dormancy, and metastatic reactivation in prostate cancer.
Citation Format: Jamie R. Schoenborn, Jing Xia, Sandy Larson, Lisha Brown, Colm Morrissey, Paul Lange, Peter S. Nelson, Robert L. Vessella, Min Fang. Establishing the use of genomic profiling on rare prostate cancer disseminated tumor cells [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 B31.