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

Background: Intra-tumor heterogeneity (ITH) encompasses cellular differences intumors and is related to clinical outcomes such as drug resistance. However, little isknown about the dynamics of ITH, owing to the lack of time-series analysis at thesingle-cell level.Results: We performed single-cell exome and transcriptome sequencing of 200 cellsand investigated how ITH is generated from one single cell in a mouse colorectalcancer model. The ITH of the transcriptome increased after transplantation fromcultured organoids, while that of the exome decreased. Mutations generated in theculture did not greatly change at the transplantation at the bulk-cell level. The RNA ITHincrease was due to the emergence of new transcriptional subpopulations. In contrastto the initial cells expressing mesenchymal-marker genes, new subpopulationsrepressed these genes at transplantation. Analyses of colorectal cancer data from TheCancer Genome Atlas revealed a high proportion of metastatic cases in humansubjects with expression patterns similar to the new cell subpopulations in mouse.These results suggest that the birth of transcriptional subpopulations may be a key foradaptation to drastic micro-environmental changes when cancer cells have sufficientgenetic alterations at later tumor stages.Conclusions: This study revealed an evolutionary dynamics of single-cell RNA andDNA heterogeneity in tumor progression, giving insights into the mesenchymal-epithelial transformation of tumor cells at metastasis in colorectal cancer.