Abstract PO5-01-09: Exploring cellular heterogeneity of localised breast cancers
Authors: Kiedik Beata , Roden Daniel , Harvey Kate , Al-Eryani Ghamdan , Wu Sunny , Hui Mun , O'Toole Sandra , Lim Elgene , Perou Charles , Swarbrick Alex 
Published: May 2024

Breast cancer is a heterogeneous disease at multiple levels, ranging from subtype differences between patients (inter-patient heterogeneity) to the diverse composition of malignant cells, heterogeneity of hormone receptor (HR) expression and cellular makeup within single breast cancer samples (intra-tumour heterogeneity). Despite an increase in the number of effective therapies available, many patients will experience an incomplete treatment response and subsequent relapse. These adverse treatment outcomes may be attributed to the often overlooked but critical factor of cellular heterogeneity.

In order to gain deeper insights into intra-tumour heterogeneity, we have applied single-cell technologies on a cohort comprising 250 primary, untreated breast cancers. We have optimized methods for tissue cryopreservation, eliminating the need for fresh sample processing, and multiplex tissue profiling. Together, these are cost-efficient processes that allow for improved handling of small tissue sizes, such as biopsies, and reduce batch effect. To ensure accurate and reliable data processing, we have developed a scalable computational workflow that includes benchmarked methods for sample SNP-demultiplexing, doublet detection, high-resolution cell annotation and cellular integration. Finally, we are extending our existing methods1 to study the cellular heterogeneity of breast cancers. Our method, scSubtyper, explores the phenotypic differences between malignant cells within tumours, by comparing each single cell to distinct features associated with different molecular subtypes and assigning each cell to one of these subtypes. Our previous study1 and preliminary results of this project revealed that over 90% of the samples exhibit a mix of malignant cells of different subtypes, and 50% of samples contain cells that have characteristics of all subtypes, demonstrating cellular heterogeneity exists not only exists between malignant cells, but also within malignant cells of a tumour. Our second approach, known as ecotyping, assesses patterns of cell type frequencies across samples and groups them based on similarity of these co-occurences. Our preliminary results have revealed the existence of 5 ecotypes that lack significant associations with samples clinical subtypes. Applying the same approach exclusively within the HR-positive samples identified 4 ecotypes characterized by distinct abundances of immune and stromal cells. This analysis revealed that ecotypes are not a simple surrogate for clinical and molecular subtypes, but their presence could drive different response to treatment.

Together, our high-throughput tissue processing and computational approaches to studying intra-tumour heterogeneity are now being applied to our large, well annotated, clinical cohort. Supported by the preliminary results, we hypothesize that this study will play a vital role in optimizing breast cancer patient stratification to improve treatment management and outcome.

1. Wu, Sunny Z., et al. "A single-cell and spatially resolved atlas of human breast cancers." Nature genetics 53.9 (2021): 1334-1347.

Citation Format: Beata Kiedik, Daniel Roden, Kate Harvey, Ghamdan Al-Eryani, Sunny Wu, Mun Hui, Sandra O'Toole, Elgene Lim, Charles Perou, Alex Swarbrick. Exploring cellular heterogeneity of localised breast cancers [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-01-09.