Abstract A059: Heterogeneous cell populations in organoid models derived from breast preinvasive and invasive carcinomas after endocrine therapy
Authors: Goldhammer Nadine , Warhadpande Shruti , Beld Liana , Maldonado Rodas Cristian K. , Lam Allison , Bui Tam Binh , Abe Shoko Emily , Alvarado Michael , Ewing Cheryl , Goodwin Karen , Mukhtar Rita , Wong Jasmine , Swigart Lamorna Brown , Hirst Gillian , Schwartz Christopher , van't Veer Laura , Esserman Laura , Chien Jo , Rosenbluth Jennifer M. 
Published: February 2024

Abstract
Approximately 80% of ductal carcinoma in situ (DCIS) and invasive breast cancers express hormone receptors (HR), and are typically treated with selective estrogen receptor modulators (SERMs) or aromatase inhibitors, or with additional HR-targeting agents in the research setting. However, the development of resistance poses a significant challenge. To better understand the mechanisms behind endocrine resistance and explore new treatment strategies, it is essential to have a reliable model system that accurately reflects the heterogeneous nature of breast lesions. In this study, we developed a protocol to generate patient-derived organoid cultures of pre-invasive and malignant breast lesions from patients with persistent or residual disease in the active surveillance or neoadjuvant setting after treatment with endocrine therapy. We generated n = 11 HR+ DCIS and n = 18 HR+ breast cancer organoids and used single-cell RNA-sequencing to characterize cell heterogeneity within individual organoid cultures. We observed mixed non-cancerous and malignant cells present within some cultures, and optimized protocols to minimize non-cancerous cell types. To better define endocrine sensitivity versus resistance, we also assessed responsiveness to estrogen and anti-estrogen therapy in individual cultures by monitoring organoid growth through live cell imaging and evaluating estrogen-response markers at the protein and RNA levels in response to treatment in vitro. Next, we applied our model system to evaluate endocrine resistance in heterogeneous tumor populations. We compared changes in cellular composition and signaling pathways in endocrine-resistant and endocrine-sensitive breast organoids based on in vitro metrics and/or correlation with clinical variables. In addition, within single cultures heterogeneous cell populations were identified with differential expression of ESR1 and HR target genes, generally falling into three cluster groups that could be defined based on different patterns of FOXA1, GATA3, TFF1, and XBP1 expression, among others. These populations also differed with evidence of co-expressed genes and signaling pathways related to breast tumorigenesis and differentiation (estrogen response, androgen response, mTOR signaling, metabolism) in putative HR-active cell populations in both pre-invasive and invasive breast cases. In summary, our study demonstrates that patient-derived breast and breast cancer organoids can be used to model estrogen responsiveness and endocrine resistance. We have established a platform that enables us to investigate the mechanisms underlying endocrine resistance at different premalignant and tumor stages to evaluate new treatment approaches. The ultimate goal of this work is to contribute to the development of new targeted therapies for endocrine-resistant breast lesions.
Citation Format: Nadine Goldhammer, Shruti Warhadpande, Liana Beld, Cristian K. Maldonado Rodas, Allison Lam, Tam Binh Bui, Shoko Emily Abe, Michael Alvarado, Cheryl Ewing, Karen Goodwin, Rita Mukhtar, Jasmine Wong, Lamorna Brown Swigart, Gillian Hirst, Christopher Schwartz, Laura van't Veer, Laura Esserman, Jo Chien, Jennifer M. Rosenbluth. Heterogeneous cell populations in organoid models derived from breast preinvasive and invasive carcinomas after endocrine therapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A059.