Integrated single-cell analysis reveals distinct epigenetic-regulated cancer cell states and a heterogeneity-guided core signature in tamoxifen-resistant breast cancer

Inter- and intra-tumour heterogeneity of breast cancer might be one of the reasons that develops endocrine therapy resistance. Here, we conduct an integrated scRNA-seq and scATAC-seq analysis of ~80K breast tissue cells from two normal (NTs), three primary (PTs) and three tamoxifen-treated recurrent tumour tissues (RTs). We identify distinct cell types among breast tumour tissues and observe a striking level of cell-to-cell heterogeneity among six tumuor tissues and delineates the primary to recurrent tumour progression, underscoring the significance of these single-cell level tumour cell clusters classified from scRNA-seq data. We then define nine cancer cell states (CSs), including five PT-specific, three RT-specific and one PT-RT-shared CSs and identify a heterogeneity-guided core signature. We further identify distinct open chromatin regions and specific transcription factors (TFs) associated with cancer cell states as well as novel biological pathways that mediate their communications with the tumour microenvironment. We finally in silico characterize the core signature and in vitro functionally examine the role of one of core signature, BMP7 suggesting that it plays an oncogenic role in tamoxifen-resistant breast cancer cells, and could be a promising therapeutic target in treating endocrine resistant breast cancer. We envision this integrated single-cell epigenomic and transcriptomic measure will become a powerful approach to unravel how epigenetic factors and tumour microenvironment govern the development of tumour heterogeneity and to uncover potential therapeutic targets that circumvent heterogeneity-related failures.