Single-cell RNA-sequencing reveals distinct patterns of cell state heterogeneity in mouse models of breast cancer.

Syn Kok Yeo,Jun-Lin Guan,Long Jason Lu,Peixin Lu,Mingang Hao,Cailian Wang,Takako Okamoto,Xiaoting Zhu

doi:10.7554/elife.58810

Abstract

Breast cancer stem cells (BCSCs) contribute to intra-tumoral heterogeneity and therapeutic resistance. However, the binary concept of universal BCSCs co-existing with bulk tumor cells is over-simplified. Through single-cell RNA-sequencing, we found that Neu, PyMT and BRCA1-null mammary tumors each corresponded to a spectrum of minimally overlapping cell differentiation states without a universal BCSC population. Instead, our analyses revealed that these tumors contained distinct lineage-specific tumor propagating cells (TPCs) and this is reflective of the self-sustaining capabilities of lineage-specific stem/progenitor cells in the mammary epithelial hierarchy. By understanding the respective tumor hierarchies, we were able to identify CD14 as a TPC marker in the Neu tumor. Additionally, single-cell breast cancer subtype stratification revealed the co-existence of multiple breast cancer subtypes within tumors. Collectively, our findings emphasize the need to account for lineage-specific TPCs and the hierarchical composition within breast tumors, as these heterogenous sub-populations can have differential therapeutic susceptibilities.

Highlights

The mammary gland is a bi-layered epithelial organ which consists of basal as well as myoepithelial cells in the outer layer
Normal mammary epithelial cell (MEC) contamination was inferred to be minimal among the cells examined (Cells without copy number variation (CNV) in Neu: 0.4%, PyMT: 0%, BRCA1-null: 8.8%) (Figure 1—figure supplement 4E–F)
PyMT tumor cells were associated with LPs of nulliparous and involution timepoints, whereas Neu tumor cells spanned the spectrum from LPs to AvPs to AvD cells

Summary

Introduction

The mammary gland is a bi-layered epithelial organ which consists of basal as well as myoepithelial cells in the outer layer. Parallels between the intrinsic molecular subtypes of breast cancer (Perou et al, 2000; Prat et al, 2010) and mammary differentiation states can be observed with basal-like breast cancers being associated with mouse fMaSCs (Pal et al, 2017; Spike et al, 2012), claudin-low breast cancers with mouse aMaSCs (Fu et al, 2017) and luminal-A breast cancers with the hormone-sensing lineage. TPCs which occupy a less-differentiated cell state could correspond to a different breast cancer subtype relative to bulk tumor cells This raises the question of whether multiple breast cancer subtypes co-exist within a tumor (Yeo and Guan, 2017). In this study, using molecular profiling and single-cell RNA sequencing (scRNA-seq) of multiple mouse models of breast cancer, we demonstrated that various tumors driven by different oncogenic events contained tumor cells spanning distinct spectra of cell states within the mammary epithelial hierarchy. The hierarchical heterogeneity that was observed in these tumors was accompanied by the co-existence of cells associated with multiple PAM50 breast cancer subtypes within each of the tumors examined

Results

Discussion

Materials and methods

Availability of data and materials