Abstract 938: Single-cell whole-genome sequencing verifies the surrogacy of circulating tumor cells for prostate cancer

Abstract

Abstract Background: Circulating tumor cells (CTCs) are rare tumor cells shed from a patient's tumors into the circulation. It has been hypothesized that CTCs could be used as a “liquid biopsy” to obtain repeat molecular characterizations and provide dynamic insight into the biology of an underlying cancer. However, due to the low abundance of CTCs and technical limitations in the single-cell sequencing, it had been very difficult to characterize CTCs on a whole genome scale. The surrogacy of CTCs for conventional tumor tissues has never been demonstrated beyond targeted genomic alterations such as shared ETS fusions in prostate cancer (PC), EGFR mutations in lung cancer and BRAF mutations in melanoma. With recent technical advances in single-cell sequencing and single-CTC isolation technologies, we present the first study using whole genome sequencing (WGS) of isolated serially-collected single CTCs in a PC patient. Method: By combining NanoVelcro CTC Chip with laser microdissection, we developed a robust platform for single-CTC isolation. Subsequent WGS was performed after the multiple displacement amplification of our single-CTC DNA. From a PC patient, we performed WGS on four of his CTCs on two different time point, his primary prostatectomy tissue and liver metastasis along with WBC and normal adjacent tissue from the prostatectomy as controls. Copy number variations, single nucleotide variations (SNVs) and structural variations (SVs), including rearrangements were identified for comparison. Results: We successfully performed WGS on isolated single CTCs, achieving 30X depth and >95% coverage. SNV analysis reveals that 33.5% (289/863) of founder somatic mutations (defined as mutations shared between primary and metastatic tumors) can be found in CTCs. Looking into the mutational landscape of CTCs, 48% of the CTC mutations can be traced back to either primary or metastatic tumor. Per SV analysis, we found and validated an intrachromosomal rearrangement in chr3 and an interchromosomal rearrangement between chr13 and chr15. These rearrangements are shared between both tumor tissues and most of the CTCs, but not discovered in WBC and normal adjacent tissue. At the same time, highly heterogeneous short SVs were discovered in PTEN, RB1 and BRCA2 in all tumor samples, suggesting a continuous evolution of SVs in these important tumor suppressor genes. Conclusion: Based on our capability to obtain high-quality WGS from single-CTCs, we validate the genomic surrogacy of CTCs by the detection of shared SNVs and rearrangements between CTCs and tumor tissues. The heterogeneous mutational landscapes of SNVs and SVs are also discovered in single-CTCs, indicating the value of our single-CTC WGS approach. We envision our single-CTC WGS approach will be utilized for studying tumor heterogeneity and the biological evolution of cancer during disease progression, even during anticancer therapy. Citation Format: Yi-Tsung Lu, Runze Jiang, Hsian-Rong Tseng, Leland WK Chung, Edwin M. Posadas. Single-cell whole-genome sequencing verifies the surrogacy of circulating tumor cells for prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 938. doi:10.1158/1538-7445.AM2014-938