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Single-cell RNA sequencing of C3(1)-Tag cancer cells during invasion and colony formation.

ABSTRACT: Purpose: Assess the cellular heterogeneity during the transition through partial EMT and MET in the spontaneous C3(1)-Tag breast cancer model. Methods: We performed MULTI-seq single cell RNA sequencing analysis in two different ex vivo assays: the collagen assay that models invasion and the colony formation assay that models metastatic outgrowth. Briefly, organoids were isolated from 4 different mice and either plated directly into collagen I matrix or further dissociated into clusters and plated into Matrigel. Cells were removed from the matrix and dissociated into single cells at day 0 (12h in matrix), day 3 and day 5. For each day, cells were barcoded by mouse and matrix and flow sorted for live cells before being processed on the 10X Genomics platform for barcoding and library construction. As a control for batch effect during library construction for the different time point, we added a cell line control (4T1) at each day. Finally, the libraries were sequenced together using the NOVAseq. Results: We sequenced 8,908 cells. After correction for batch effect, we performed a pseudotime analysis. We observed a temporal progression of the cells during invasion and colony formation. This transition is associated with a decrease in E-cadherin and an increase in vimentin expressions as well as other EMT genes during invasion and the opposite during colony formation. These results demonstrated at the single cell resolution that there is a temporal progression associated with EMT and MET during invasion and colony formation, respectively.

ORGANISM(S): Mus musculus

PROVIDER: GSE149299 | GEO | 2022/08/15

REPOSITORIES: GEO

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Single-cell RNA sequencing of C3(1)-Tag cancer cells during invasion and colony formation.

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