Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model

Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes, such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of time-series analysis at the single-cell level. We performed single-cell exome and transcriptome sequencing of 200 cells and investigated how ITH is generated from one single cell in a mouse colorectal cancer model. The ITH of the transcriptome increased after transplantation from cultured organoids, while that of the exome decreased. The RNA ITH increase was due to the emergence of new transcriptional subpopulations. In contrast to the initial cells expressing mesenchymal-marker genes, new subpopulations repressed these genes at transplantation, suggesting that the birth of transcriptional subpopulations without substantial genetic changes is associated with mesenchymal-epithelial transformation at metastasis. Analyses of colorectal cancer data from The Cancer Genome Atlas, revealed a higher proportion of patients with metastatic tumor among human subjects with expression patterns similar to those of mouse cell subpopulation. This study revealed an evolutionary pattern of single-cell RNA and DNA changes in tumor progression, giving clinical insights into the mesenchymal-epithelial transformation of tumor cells and subclasses of colorectal cancer.