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. Ó2017 AACR.

Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol

“…For this reason, single-cell analysis has proved to be very useful for the study of cellular subpopulation in many solid human tumors, such as breast [ 1 ], kidney [ 2 ], colon [ 3 ] and prostate [ 4 ] cancers.…”

“…It has been shown that the temporal order in which mutations accumulate in hematological neoplasms and in many solid human tumors, such as breast [ 1 ], kidney [ 2 ], colon [ 3 ] and prostate [ 4 ] cancers, is fundamental to understand the clonal landscape underlying disease evolution. In recent years, single-cell genomics has been developed as a powerful method for reconstructing the complex cancer pathogenesis [ 5 ] and its heterogeneity.…”

Copolymerization of single-cell nucleic acids into balls of acrylamide gel

“…We used single-nuclei DNA data previously generated from a previous WGA method (Alexander et al 2018). Briefly, single nuclei were deposited into individual wells in a 96-well plate and amplified using GenomePlex WGA4 kit (Sigma-Aldrich WGA4-50RXN) according to the manufacturer's instructions.…”

“…The method works on nuclei isolated from frozen tumor biopsies, and we illustrate this using previously published clinical material (Alexander et al 2018). Figure 2C shows the pathology image of a region from a prostate with a Gleason 9 lesion, assessed by pathologists as 60% cancer.…”

“…In the experiments, we used a normal skin fibroblast cell strain (SKN1) and three breast tumor cell lines (SK-BR-3, BT-20, and MCF-7). Clinical specimens were as previously cited (Alexander et al 2018). In particular, a tissue biopsy was obtained from a patient (COR003.GS9.2) undergoing radical prostatectomy (RP) at New York-Presbyterian/Weill Cornell Medical Center.…”