Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects

Abstract

Advances in genomic technology have enabled the faithful detection and measurement of mutations and the gene expression profile of cancer cells at the single-cell level. Recently, several single-cell sequencing methods have been developed that permit the comprehensive and precise analysis of the cancer-cell genome, transcriptome, and epigenome. The use of these methods to analyze cancer cells has led to a series of unanticipated discoveries, such as the high heterogeneity and stochastic changes in cancer-cell populations, the new driver mutations and the complicated clonal evolution mechanisms, and the novel identification of biomarkers of variant tumors. These methods and the knowledge gained from their utilization could potentially improve the early detection and monitoring of rare cancer cells, such as circulating tumor cells and disseminated tumor cells, and promote the development of personalized and highly precise cancer therapy. Here, we discuss the current methods for single cancer-cell sequencing, with a strong focus on those practically used or potentially valuable in cancer research, including single-cell isolation, whole genome and transcriptome amplification, epigenome profiling, multi-dimensional sequencing, and next-generation sequencing and analysis. We also examine the current applications, challenges, and prospects of single cancer-cell sequencing.

Single Cell Isolation and Analysis

“…Several important types of cancer cells have been discovered, including primary tumor cells, metastatic tumor cells, cancer stem cells (CSC), circulating tumor cells (CTC), and disseminated tumor cells (DTC) (Zhang et al, 2016). CTC and DTC play a vital role in cancer dissemination, self-renewal, and distant metastases.…”

Mechanisms that drive inflammatory tumor microenvironment, tumor heterogeneity, and metastatic progression

“…It has led to a series of unanticipated discoveries, such as high heterogeneity and stochastic changes in cancer-cell populations, new driver mutations, and molecular mechanisms of clonal evolution [172]. RNAseq from 4645 single cells isolated from 19 patients with melanoma showed transcriptional heterogeneity in tumor cells, as well as distinct TME patterns, including exhaustion of tumor-infiltrating T cells [173].…”

Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA)

“…Accumulating clinical studies during the past few years suggest that circulating tumor cells (CTCs) exert a critical role in cancer dissemination, organ invasion and distant metastases (1). The biological process of transformation from a normal somatic cell to a cancer cell is characterized by a variable number of selective gene mutations specific for clonal evolution, diversity and metastatic capacity (2)(3)(4).…”