Transcriptome analysis has been extensively used to understand the heterogeneity of breast tumours, defining intrinsic molecular subtypes and signatures able to predict response to therapy and patient outcome. This molecular phenotyping has fostered crucial therapeutic advances. However, cancer cell diversity constitutes a challenge for cancer treatment and deeply impact the outcome of cancer patients. A simultaneous overview of cancer cells and associated stromal cells is critical for the design of improved therapeutic regimes.
Single-cell RNA-seq has emerged as a powerful method to unravel heterogeneity of complex biological systems; this has enabled in vivo characterization of cell type compositions through unsupervised sampling and modeling of transcriptional states in single cells. Here we use the high-throughput microfluidic-based single-cell RNA-seq method Drop-seq to elucidate the function and cellular composition of breast tumours. We use the MMTV-PyMT mouse mammary tumour model to provide high-resolution landscapes of the disease progression, delivering simultaneous observation of cellular events that result in the acquisition of the metastatic phenotype. We define transcriptional networks that result in acquired immune tolerance, extracellular matrix remodelling and progression to metastatic disease. The unprecedented resolution generated by analysis 40,000 individual tumour cells revealed dynamics and plasticity of cancer cells during progression to metastatic disease. Finally, we studied the functional consequences of identified cell signatures of well-known key events during breast cancer progression, EMT, collagen deposition, inflammation and hypoxia.
In summary, we provide a large-scale single-cell transcriptional landscape of breast tumours that allows unprecedented understanding of breast heterogeneity and deep analysis of the events that result in cancer progression. scRNA-seq technology is generating a paradigm-shift in our understanding of biology, applied to tumour biology will lay the first stone for the development of more specific cancer therapies.