A comparison of isolated circulating tumor cells and tissue biopsies using whole-genome sequencing in prostate cancer

Abstract

Previous studies have demonstrated focal but limited molecular similarities between circulating tumor cells (CTCs) and biopsies using isolated genetic assays. We hypothesized that molecular similarity between CTCs and tissue exists at the single cell level when characterized by whole genome sequencing (WGS). By combining the NanoVelcro CTC Chip with laser capture microdissection (LCM), we developed a platform for single-CTC WGS. We performed this procedure on CTCs and tissue samples from a patient with advanced prostate cancer who had serial biopsies over the course of his clinical history. We achieved 30X depth and ≥ 95% coverage. Twenty-nine percent of the somatic single nucleotide variations (SSNVs) identified were founder mutations that were also identified in CTCs. In addition, 86% of the clonal mutations identified in CTCs could be traced back to either the primary or metastatic tumors. In this patient, we identified structural variations (SVs) including an intrachromosomal rearrangement in chr3 and an interchromosomal rearrangement between chr13 and chr15. These rearrangements were shared between tumor tissues and CTCs. At the same time, highly heterogeneous short structural variants were discovered in PTEN, RB1, and BRCA2 in all tumor and CTC samples. Using high-quality WGS on single-CTCs, we identified the shared genomic alterations between CTCs and tumor tissues. This approach yielded insight into the heterogeneity of the mutational landscape of SSNVs and SVs. It may be possible to use this approach to study heterogeneity and characterize the biological evolution of a cancer during the course of its natural history.

Single-Cell Analysis of Circulating Tumor Cells as a Window into Tumor Heterogeneity

“…Thus, we found that complex and heterogeneous drug resistance mechanisms exist in advanced prostate cancer, as revealed by the study of heterogeneous populations of CTCs. The degree of heterogeneity observed in CTCs in CRPC patients is consistent with intratumoral heterogeneity observed in patients with advanced metastatic prostate cancer, suggestive of the polyclonal seeding of divergent clones (Lohr et al 2014; Gundem et al 2015; Jiang et al 2015), and is reflective of the variety of molecular alterations that may occur in parallel in tumor cells during disease progression and the development of resistance to therapy.…”

Tumour Heterogeneity: The Key Advantages of Single-Cell Analysis

“…These studies include that by De Luca et al, in which inter- and intra-patient heterogeneity is observed in the mutational status of breast cancer CTCs analysed by NGS [101]. In addition, there have been studies comparing CTCs and metastases or primary tumours at the single-cell level, such as the study performed by Jiang et al in which they discovered highly heterogeneous short structural variants of PTEN, RB1, and BRCA2 in all tumour and CTC prostate samples assessed using high-quality WGS [102]. Interestingly, Powell et al performed one of the first studies in CTCs focused on single-cell transcriptomes.…”

Materials and microfluidics: enabling the efficient isolation and analysis of circulating tumour cells

“…128,150 Recently, a modified assay has been reported, which consists of pre-labelling a RBC lysed blood sample with biotinylated Abs and recovering the labeled cells with the streptavidin-coated device. 52,148 Cell line recoveries were shown to be 65–93% depending on EpCAM expression (Table 1). 148 …”