Single-cell RNA Sequencing Reveals The Cellular Origin And Evolution Of Breast Cancer In BRCA1 Mutation Carriers

Purpose:Women with germline mutations in the BRCA1 gene have a greatly increased risk of developing breast cancer and exhibit a predisposition for the development of aggressive basal-like breast tumors,while the mechanism underlying the tissue-specific and phenotypespecific carcinogenesis remains unclear.Recently multiple lines of evidence supported a crucial role for BRCA1 in mammary epithelial cell differentiation,led to the speculation that the predisposition for developing basal-like tumors in BRCA1 carriers may result from cellular distinctions present prior to neoplastic transformation.Method:We performed single-cell RNA sequencing on 82,122 cells isolated from the breast cancer tissues and the adjacent and/or prophylactic normal breast tissues from four BRCA1 mutation carriers and three non-carriers.Whole-exome sequencing was performed on breast tumors from the four BRCA1 mutation carriers,and bulk RNA sequencing,inmmunohistochemistry and immunofluorescence staining was performed on adjacent normal breast tissues from eight additional BRCA1 mutation carriers and fourteen non-carriers for validation.Results:By comparing the expression profile in single-cell level between breast cancer cells and normal epithelial cells from BRCA1 mutation carriers,our study revealed that ERhigh tumor cells had the highest similarity to mature luminal cells,while ERneg tumor cells had the highest similarity to luminal progenitor cells.these scRNA-seq data indicated the correlation between cell of origin of ERneg/ERhigh tumors and luminal progenitor/mature luminal cell in BRCA1 mutation carriers,which were also validated by the bulk RNA-seq data of eighteen breast cancers in BRCA1 mutation carriers from the TCGA dataset.In addition,our study revealed the aberrant proportions and abnormal expression profile of epithelial cells in normal breast tissues from BRCA1 mutation carriers.The aberrant luminal progenitor cells with impaired differentiation were remarkably increased in normal breast tissues in BRCA1 mutation carriers compared with non-carriers.These observations were further validated by the bulk RNA sequencing data from additional BRCA1 mutation carriers.The expression of TP53 and BRCA1 was decreased,while epithelial-mesenchymal transition was upregulated in luminal progenitor cells from normal breast tissue in BRCA1 mutation carriers,and the mesenchymal features in the basal-like cancer cells were further upregulated compared with the luminal progenitor cells,which might result in basal-like tumors(ERneg)development.The expression of GATA3,PR and TFF1(hormone response genes)was decreased in mature luminal cells from normal breast tissue in BRCA1 mutation carriers,indicating the impaired differentiation of mature luminal cells in BRCA1 mutation carriers.In addition,these differentiation processes were further downregulated in ERhigh tumor cells compared with mature luminal cells in BRCA1 mutation carriers,indicating that the impaired differentiation of mature luminal cells in BRCA1 mutation carrers might contribute to tumorigenesis.Conclusions:In summary,our scRNA-seq data provided in-depth evidence for the putative cellular origin and evolution of breast cancers in BRCA1 mutation carriers.We revealed that the aberrant luminal progenitors might contribute to basal-like breast cancers through upregulation of basal/mesenchymal features during and even before tumorigenesis,while ERhigh luminal tumors might originate from mature luminal cells,respectively.These findings may shed light on the current understanding of breast tumor susceptibility and development in BRCA1 mutation carriers and are useful for developing new targeted prevention strategies.