The analysis of single cancer cells has transformed from qualitative microscopic images to quantitative genomic datasets

The analysis of single cancer cells has transformed from qualitative microscopic images to quantitative genomic datasets. hybridization (FISH), galvanized the field by allowing researchers to visualize the genomic diversity of chromosome aberrations directly in single tumor cells [2C4]. However, only in the past four years has the field moved from qualitative imaging data to quantitative datasets that are amenable to statistical and computational analysis. This paradigm shift has largely been fueled by the development of whole-genome amplification (WGA) and whole-transcriptome amplification (WTA), methods that can amplify the genome or transcriptome of a single cell from picogram-to-microgram quantities. By combining these methods with next-generation sequencing (NGS) technologies, it is now possible to obtain genome-wide mutational and transcriptional datasets on individual malignancy cells. Single-cell sequencing (SCS) Rabbit Polyclonal to MAK (phospho-Tyr159) promises to address key issues in cancer research, including resolving intratumor heterogeneity, tracing cell lineages, understanding rare tumor cell populations and measuring mutation rates. Such investigations were previously difficult to perform by sequencing bulk tissue samples, as these are limited to providing an average signal from a complex populace of cells. While some clonal diversity can be resolved by deconvoluting deep-sequencing data [5C7] and sequencing different spatial regions of tumors [8], the data still reflect an admixture signal. The presence of multiple clonal subpopulations and rare tumor cells is certainly difficult to solve from these data, and perseverance of which combos of mutations can be found in any provided cell can be hard to solve. As well as the genomic heterogeneity within tumors, there’s phenotypic heterogeneity also, which may be due to genomic mutations, or through epigenetic adjustments, transcriptional changes, modifications in proteins proteins or amounts adjustments. Most notably, many solid tumors display evidence of harboring both epithelial and mesenchymal populations, the second option of which are often referred to as malignancy stem cells. These stem-like cells are clear progenitors in hematopoietic cancers, but remain a controversial subject with respect to most solid tumors [9C11]. While there is considerable evidence that tumor cells can communicate with their neighbors and the stroma, there are also many complex biological processes that occur through the actions of individual malignancy cells. These processes include the initial transformation event in a normal cell, clonal growth within the primary tumor, metastatic dissemination and the development of chemoresistance (Number?1). SCS provides a powerful new approach to study the genomic and transcriptomic basis of these processes directly in human cancers, without the necessity for model organisms. Open in a separate window Number 1 Single-cell processes in malignancy. Although single malignancy cells interact with their neighbors and the adjacent stromal cells, there are many biological processes that occur through the actions of individual malignancy cells, shown with this illustration. These complex biological processes in human cancers include: (a) transformation from a single normal somatic cell into a tumor cell; (b) clonal development that occurs through a series of CGK 733 selective sweeps when solitary cells acquire driver mutations and diversify, leading to intratumor heterogeneity; (c) solitary cells from the primary tumor intravasate into the circulatory system and extravasate at distant organ sites to form metastatic tumors; and (d) the development of chemoresistance that occurs when the tumor is definitely eradicated but survived by solitary tumor cells that harbor resistance mutations and expand to reconstitute the tumor mass. With this review, we discuss how SCS methods are helping to handle fundamental questions in malignancy biology, including: what CGK 733 is the range and degree of clonal diversity in human cancers? Do tumors evolve from solitary cells in normal cells, or from multiple cells? Do tumor cells have an increased mutation rate relative to normal cells? Which clones are responsible for metastatic dissemination and growing resistance to chemotherapy, and are they rare? Several groups possess begun to address questions such as these by using SCS in a number of malignancies, but many specialized hurdles still stay in order to CGK 733 tell apart real biological variety from technical mistakes. We are going to discuss the caveats and advantages. CGK 733