Oral Presentation 32nd Lorne Cancer 2020

An integrated multi-omic cellular atlas of primary human breast cancers (#10)

Daniel L Roden 1 2 , Sunny Wu 1 2 , James Torpy 1 2 , Kate Harvey 2 , Ghamdan Al-Eryani 1 2 , Nenad Bartonicek 1 2 , Aatish Thennavan 3 , Simon Junankar 1 2 , Chia-Ling Chan 2 , Aurelie Cazet 1 2 , Mun Hui 1 2 4 , Rui Hou 5 , Alistair Forrest 5 , Davendra Segara 6 , Andrew Parker 6 , Cindy Mak 4 , Jane Beith 4 , Belinda Chan 4 7 , Hugh Carmalt 7 , Laurence Gluch 8 , Elizabeth Robbins 9 , Sanjay Warrier 4 9 , Charles Perou 3 , Elgene Lim 1 2 6 , Sandra O'Toole 1 2 10 , Alexander Swarbrick 1 2
  1. St Vincent's Clinical School, University of New South Wales, Sydney
  2. The Kinghorn Cancer Centre, Garvan Institute, Sydney, NSW, Australia
  3. UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, United States
  4. The Chris O'Brien Lifehouse, Sydney
  5. Harry Perkins Institute, Perth
  6. St Vincent’s Hospital, Sydney, NSW
  7. Strathfield Private Hospital, Sydney
  8. The Strathfield Breast Centre, Sydney
  9. Royal Prince Alfred Hospital, Sydney
  10. Australian Clinical Laboratories, Sydney, NSW

Solid cancers are a complex ‘ecosystem’ of diverse cell-types, whose interactions between malignant epithelial, stromal and immune populations are central in defining disease aetiology and response to therapy. Breast cancer is heterogenous and the complexity of the tumour microenvironment, and its interaction with malignant epithelial cells, remains poorly characterized. This limits the development of effective targeted therapies. 

To systematically profile the cellular diversity of breast cancers, single-cell RNA sequencing (scRNA-Seq) was applied to 26 primary tumours, spanning all major molecular subtypes. We integrated transcriptomes from over 150,000 individual cells, providing a high-resolution characterization of the neoplastic, immune and stromal landscapes. CITE-SEQ was used on representative cases to profile ~150 cell-surface proteins within the tumour microenvironment. Integrating these modalities identified distinct and novel immune and stromal cellular states that may play critical roles in regulating cancer progression.

Transcriptional heterogeneity of malignant epithelial cells is observed both within and between breast tumours and is an important clinical factor. Further, we have identified confounding mixtures of entrapped normal and malignant epithelial cells within individual tumours. Matched spatial profiling confirms these observations. Large-scale copy-number changes were inferred in each cell to isolate malignant epithelial cells. To explore their transcriptional heterogeneity we developed a single-cell specific extension of the PAM50 molecular subtype classifier, and a meta-gene approach to characterize the regulatory programs of tumour cell-states. Together, these complementary approaches, for the first time, describe distinct and recurring cancer cell populations across diverse breast tumours.

Our study highlights the potential of atlas-scale single-cell projects to unravel the complex cellular heterogeneity within tumours and identify novel cell types and regulatory states underlying carcinogenesis. Such insights will guide the next-generation of therapies, which will likely be based upon an integrated understanding of the neoplastic, stromal and immune states that define a tumour and inform treatment response.