Abstract 6232: Defining the cellular composition and associated molecular phenotypes of malignant and non-malignant cells in breast cancer pleural effusions
Authors: Whitfield Holly J. , Berthelet Jean , Mangiola Stefano , Bell Caroline , Anderson Robin L. , Pal Bhupinder , Papenfuss Anthony T. , Yeo Belinda , Merino Delphine , Davis Melissa J. 
Published: June 2022

Abstract
Malignant pleural effusions (MPE) are a common complication of advanced cancers, particularly those adjacent to the pleura such as lung and breast cancer and are a frequent complication in metastatic disease. The pathophysiology of MPE formation in advanced breast cancer remains poorly understood, and their composition and biology are understudied. To characterise the phenotypic diversity of malignant pleural effusion, we performed single-cell RNA sequencing on 10 MPEs from 7 metastatic breast cancer patients with diverse molecular subtypes: two triple negative (TNBC) patients, three luminal B patients including one with a rare inflammatory subtype, and two luminal A patients. For all patients, we sequenced cells from the entire MPE, without performing any enrichment or selection, in order to ascertain the cellular composition and molecular phenotypes in an unbiased manner. We identified pronounced differences in the relative proportions of malignant, mesothelial and immune cell populations: both TNBC and two Luminal B patients had extensive malignant cell populations, while the other three patients had few or no detectible malignant cells but extensive immune populations. We also observed heterogeneity in the expression of subtype-specific gene signatures and in copy number aberration patterns that captured variability across malignant cell populations both within and between patients. We observed that most malignant cells retained the molecular subtype diagnosed in the primary tumour, however sub-populations of malignant cells could be identified that mapped to different molecular subtypes, indicative of complexity in the molecular phenotypes of cancer cells disseminated to or metastasising in the pleural cavity. We distinguished mesothelial cell populations from malignant cells using key markers, expression of the PAM50 signatures, and copy number aberration patterns. We found that pleural mesothelial cells expressed a cancer associated fibroblast-like transcriptomic program that may support cancer growth within the pleural cavity through the secretion of growth factors that target malignant cells. Our dataset presents the first unbiased and unselected assessment of breast cancer associated MPEs at single cell resolution, providing the community with a vital resource for the study of MPEs. Our work highlights the molecular and cellular diversity captured in MPEs and advances the use of these clinically relevant biopsies both in monitoring disease progression and in the development of targeted therapeutics for patients with advanced breast cancer.
Citation Format: Holly J. Whitfield, Jean Berthelet, Stefano Mangiola, Caroline Bell, Robin L. Anderson, Bhupinder Pal, Anthony T. Papenfuss, Belinda Yeo, Delphine Merino, Melissa J. Davis. Defining the cellular composition and associated molecular phenotypes of malignant and non-malignant cells in breast cancer pleural effusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6232.