Breast cancers are a complex ‘ecosystem’ of diverse cell types, whose heterotypic interactions play central roles in defining the aetiology of disease and its response to therapy. However, our poor understanding of the tumour microenvironment (TME) of breast cancers has limited the development and implementation of new drugs that target stromal and immune cells.
We have used multi-dimensional single cell genomics to characterise more than 150,000 cells collected from a unique cohort of 32 early and metastatic breast cancers with rich clinico-pathological annotation. Malignant cells showed remarkable intra-tumoural heterogeneity for canonical breast cancer features, such as intrinsic subtype, hormone receptor expression and activity, drug targets, drug resistance signatures and transcriptional drivers.
Cancer Associated Fibroblasts (CAFs), which are classically studied as a single cell type, were heterogeneous across primary and metastatic sites. Interestingly we identified a myofibroblast-like subset and an inflammatory-mediator subset and propose multi-faceted roles in regulating malignancy and tumour immunity. Distinct transcription factor networks regulated these polarised states.
We applied a new method known as CITE-Seq to measure more than 100 cell surface markers and checkpoint proteins in addition to single cell RNA-Sequencing. We resolve the tumour-immune milieu with high precision and generate new transcriptional signatures of breast tumour-infiltrating leukocytes.
To track cellular clonal dynamics through space and time, we developed a novel method known as RAGE-Seq to permit simultaneous analysis of transcriptomes and targeted full length nanopore sequencing at single cell resolution. Using this method to sequence lymphocyte receptors, we observe clonal expansion and trafficking of CD4+ and CD8+ T lymphocytes between the lymph nodes, blood and tumor of patients.
By implementing and developing new single cell genomic methods, we have obtained extensive new insights into the cellular landscape of breast cancer, which will reveal new biomarkers and opportunities for stromal- and immune-based therapy.