Abstract GS1-01: Landscape of the breast tumour microenvironment at single-cell resolution

Abstract

Breast cancers are a complex 9ecosystem9 of diverse cell types, whose heterotypic interactions play central roles in defining the aetiology of disease and its response to therapy. The next generation of therapies will likely be based upon an integrated understanding of the malignant, microenvironmental and immune states that define the tumour and inform treatment response. 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. Single cell genomics (SCG) is a remarkable new platform to examine the compositional, gene expression and other parameters of thousands of cells, rapidly and at scale. We have used a multi-dimensional SCG approach to characterise the TME in a unique cohort of early and metastatic breast cancers with rich clinico-pathological annotation. We have conducted single cell RNA-Sequencing on more than 125,000 cells collected from 22 patients. 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 cell surface immune markers and checkpoint proteins simultaneous to RNA-Sequencing. We resolve the tumour-immune milieu with high precision and generate new transcriptional signatures of breast tumour-infiltrating leukocytes. To track lymphocyte clonal dynamics through space and time, we developed a novel method known as RAGE-Seq to permit simultaneous full length lymphocyte receptor- and RNA-sequencing at single cell resolution. We observe clonal expansion and trafficking of CD4+ and CD8+ T lymphocytes between the lymph nodes, blood and tumor of patients. In comparison, B cells were polyclonal, suggesting an absence of antigen-dependent clonal expansion. This data provides by far the most extensive insights into the cellular landscape of breast cancer and will reveal new biomarkers and opportunities for stromal- and immune-based therapy. Citation Format: Swarbrick A, Wu SZ, Roden D, Al-Eryani G, O9Toole S, Lim E. Landscape of the breast tumour microenvironment at single-cell resolution [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr GS1-01.