Genetic Heterogeneity of Gleason Score 7 Prostate Cancer: A Pilot Study of the Canadian Prostate Cancer Genome Network (CPC-GENE)
Dominique Trudel, Michael Fraser, Emilie R Lalonde, Alice Meng, Andrew Brown, Taryne Chong, Amin Zia, Michelle Sam, Pablo H Hennings-Yeomans, Fouad Yousif, Rob Denroche, Jeremy Johns, Lee Timms, Nicholas Buchner, Richard de Borja, Nicholas J Harding, Michelle A Chan-Seng-Yue, Jianxin Wang, Gaetano Zafarana, Maud HW Starmans, Melania Pintilie, Neil Fleshner, Stanislav Volik, Lakshmi Muthuswamy, Colin C Collins, Thomas J Hudson, Lincoln D Stein, Timothy Beck, John D McPherson, Theo van der Kwast, Paul C Boutros, Robert G Bristow. University of Toronto, Toronto, Canada; University of British Columbia, Vancouver, Canada
Background: Despite the use of Gleason score as the most important prognostic factor in prostate cancer (CaP), our genetic studies using aCGH have shown that tumors with the same Gleason score can vary 100 fold in genetic instability. Furthermore, CaP is a multifocal and, likely, a multi-clonal disease as reflected in part by the heterogeneity in TMPRSS2:ERG fusion status in different tumor foci from a single prostate. In the era of personalized medicine, there is an urgent need to characterize inter- and intra-prostate molecular heterogeneity for patient stratification.
Design: The Canadian Prostate Cancer Genome Network (CPC-GENE) has undertaken a pilot study to provide an evaluation of the heterogeneity in Gleason score 7 PCa using a robust genomic approach. Gleason score (GS) 4+3 and 3+4 tumors from 5 frozen radical prostatectomies were analyzed using whole-genome sequencing (WGS) and Affymetrix OncoScan SNP arrays to determine differential genetic signatures. DNA from formalin-fixed, paraffin-embedded (FFPE) foci from the prostatectomies was analyzed by WGS after tumor mapping according to histopathology characteristics, including ERG immunostaining. Tumor foci were manually macrodissected before DNA extraction. For each patient, germline DNA from whole blood was used as a control.
Results: A total of 28 tumor foci from 5 prostates were sequenced (frozen: 5; FFPE: 18). Across multiple specimens, single nucleotide variants (SNVs) and copy number variations (CNVs) identified using WGS were validated with ∼98% accuracy against the OncoScan platform. Analysis of germline SNV profiles suggests a concordance of ∼99% between tumor regions (∼3.7 million germline SNVs/patient). A median of 55 somatic SNVs were identified in the 28 foci (interquartile range: 36-75) and nearly all SNVs were unique to a tumor focus. CNV profiles were heterogeneous among the cases. In two cases with > 4 sequenced foci, CNVs segregated according to localization in the prostate. In one case with 4 ERG-positive and 4 ERG-negative foci, the SNV profiles of the foci segregated according to ERG status. Sub-clonal phylogenetic analyses revealed evidence of independent tumor origins in at least one case.
Conclusions: The number of identified variants suggests a high degree of intra-focal and intra-prostatic genetic heterogeneity in GS7 PCa, and we brought further information about PCa intraprostatic phylogeny. This could be important both in the identification of the significant tumor focus and in the capacity to act on targetable mutations.
Category: Special Category - Pan-genomic/Pan-proteomic approaches to Cancer
Monday, March 4, 2013 9:30 AM
Poster Session I Stowell-Orbison/Surgical Pathology/Autopsy Awards Poster Session # 279, Monday Morning