Abstract 6373: Spheroid culture of ER+ breast cancer patient-derived tumor cells enriches cancer stem-likecells with EpCAM-/CD49f+and high ALDH activity and poor prognostic gene signatures
Authors: Kim Hoe Suk , Ryu Seungyeon , Yoon So-Hyun , Lee Sangeun , Song Junhyuk , Choi Yoonjung , Baek Moonjou , Lee Han-Byoel , Jon Sangyong , Lee Daeyoup , Han Wonshik 
Published: June 2022

Abstract
Background: Cancer stem-like cells (CSCs) represent a critical subset of the tumor population, which contributes to tumor recurrence, metastasis and therapy resistance. Spheroid culture is unique method for CSC enrichment. Patient-derived breast cancer cells (PDBCCs) has provided an invaluable tool in preclinical and translational research. The objective of this study is to characterize the immunophenotype and transcriptomes of PDBCCs grown in the adherent monolayer and spheroid condition.
Methods: PDBCCs were harvested from residual tumor of fresh surgical specimens of patients with ER-positive subtype (8 cases). The adherent monolayer(M) and spheroid(S) culture of PDBCCs were applied on collagen I-coated plate and an ultra-low attachment polymer-X coated plate. Flow cytometry and immunocytochemistry was performed by using fluorescent-dye conjugated antibodies for EpCAM, CD49f, CD24, CD44, and cytokeratin. ALDEFLUOR® assay to detect ALDH activity was used. Total RNA-sequencing was applied to investigate differentially expressed genes (DEGs), followed by GO and KEGG pathway enrichment analysis. Real-time RT-PCR was performed to evaluate BCSC-related RNA levels. The Kaplan-Meier Plotter online database was used to evaluate the prognostic value of DEGs (2-fold change, p&lt;0.05).
Results: Under adherent monolayer condition, more than 95% of PDBCCs passaged for up to 5 passages on collagen I-coated plate sustained EpCAM+/cytokeratin+/fibroblast marker_ phenotype. On polymer-X coated plates, PDBCCs formed compact multicellular spheroids with a diameter of less than 300 µm. As compared with monolayer, CSCs with EpCAM-/CD49f+ phenotype (M vs S; 0.16±0.06 vs 2.34±0.65, p=0.015) and high ALDH activity (M vs S; 0.73±0.43 vs 7.05±1.48, p=0.038) were significantly increased by spheroid culture. In whole-transcriptome analysis (3 cases) between spheroid and monolayer, a total of 561 DEGs were identified, including 290 upregulated and 271 downregulated DEGs (2- fold change, p&lt;0.05) in spheroid. The upregulated and downregulated DEGs in spheroids were enriched in 8 and 19 KEGG pathways, respectively. In recurrence-free survival analysis based on the Kaplan-Meier Plotter database of the genes corresponding to Oncotype Dx, Mammaprint, and Prosigna and top 30 ranked DEGs identified in spheroids, 15 upregulated and 14 downregulated DEGs were associated with poor prognosis of breast cancer patients.
Conclusion: Spheroid culture of PDBCCs with ER+ subtype enriches CSCs and poor prognostic gene signatures. Future studies to explore the specific molecular mechanisms underlying these observations may provide new molecular targets for the development of therapies for targeting CSCs in breast cancer patient.
Citation Format: Hoe Suk Kim, Seungyeon Ryu, So-Hyun Yoon, Sangeun Lee, Junhyuk Song, Yoonjung Choi, Moonjou Baek, Han-Byoel Lee, Sangyong Jon, Daeyoup Lee, Wonshik Han. Spheroid culture of ER+ breast cancer patient-derived tumor cells enriches cancer stem-likecells with EpCAM-/CD49f+and high ALDH activity and poor prognostic gene signatures [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 6373.