Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer

Abstract

A distinction between indolent and aggressive disease is a major challenge in diagnostics of prostate cancer. As genetic heterogeneity and complexity may influence clinical outcome, we have initiated studies on single tumor cell genomics. In this study, we demonstrate that sparse DNA sequencing of single-cell nuclei from prostate core biopsies is a rich source of quantitative parameters for evaluating neoplastic growth and aggressiveness. These include the presence of clonal populations, the phylogenetic structure of those populations, the degree of the complexity of copy-number changes in those populations, and measures of the proportion of cells with clonal copy-number signatures. The parameters all showed good correlation to the measure of prostatic malignancy, the Gleason score, derived from individual prostate biopsy tissue cores. Remarkably, a more accurate histopathologic measure of malignancy, the surgical Gleason score, agrees better with these genomic parameters of diagnostic biopsy than it does with the diagnostic Gleason score and related measures of diagnostic histopathology. This is highly relevant because primary treatment decisions are dependent upon the biopsy and not the surgical specimen. Thus, single-cell analysis has the potential to augment traditional core histopathology, improving both the objectivity and accuracy of risk assessment and inform treatment decisions.Significance: Genomic analysis of multiple individual cells harvested from prostate biopsies provides an indepth view of cell populations comprising a prostate neoplasm, yielding novel genomic measures with the potential to improve the accuracy of diagnosis and prognosis in prostate cancer. Cancer Res; 78(2); 348-58. ©2017 AACR.

Figure 1. Single cell genomic viewer (SCGV) images for the case NYU007.GS7.2

SCGV is an interactive and integrative tool for data visualization built in Python. Panel A is an illustration of the prostate, a walnut sized organ, in which a dozen or more biopsies are taken, and single isolated nuclei prepared from each location. The copy number profiles are determined from low coverage sequence, and arranged in a phylogenetic tree. Panel B is one level of the viewer, showing the profiles for each of several hundred nuclei as columns, integrated with information about the sector location, sector pathology, ploidy and noise. From this level, one can call up at various scales portions of the populations (panel C), or reorder the heat map by sector (Panel D). One can view groups of profiles in greater detail, and at any scale (Panels E - G). From here one can open the UCSC Genome Browser to view the genetic loci with annotation (Panel H), which in this case illustrates that an early event in the ontogeny of this cancer has been a homozygous deletion of the CHD1 gene.

Figure 2. Clonal structure and spread

Clonal structure is represented as a tree, alongside with a schematic depiction of the diagnostic prostate biopsy, for the six diagnostic-biopsy cases in which clones were identified. For each tree, the number of cells analyzed by sparse sequencing is represented at each node, with all cells at the root. Clones and sub-clones are shown as colored nodes of the tree, with the number of cells sampled from each indicated. To the right of each tree, a schematic cross-section of the prostate is shown, with the locations of origin for the standard 12-core biopsy scheme depicted as circles, and the locations of the additional MRI-guided biopsies depicted as squares. The fill colors at each location correspond to the clones and sub-clones found therein. Cores with pathological finding of malignancy but no clonal populations detected are indicated by “+”. Cores with clonal populations detected but no pathological finding of malignancy are indicated by “N” nearby.