Abstract 6269: Advanced single-cell RNA-seq reveals complex interactions between circulating tumor cells and immune subtypes in prostate cancer

Abstract Background: Prostate cancer is marked by extensive cellular diversity within its tumor microenvironment (TME), significantly impacting disease progression and responses to treatment. The study aims to dissect this heterogeneity at the single-cell level, identify distinct subpopulations within key cell types such as circulating tumor cells (CTCs) and T lymphocytes, and uncover potential therapeutic targets. Methods: We analyzed single-cell RNA-seq data from 16 prostate cancer samples, which included over 170, 000 cells. Initially, we performed data integration and normalization using Reciprocal Principal Component Analysis (R-PCA) to mitigate batch effects and enhance data quality. For dimensionality reduction, both PCA and UMAP (Uniform Manifold Approximation and Projection) were applied, allowing us to visualize and identify patterns in the high-dimensional dataset. Clustering of cells was conducted using the k-means algorithm to categorize cells into distinct clusters based on their gene expression profiles. Finally, cell type classification within these clusters was achieved using Support Vector Machines (SVMs), enabling the precise identification of cellular identities and states based on their molecular signatures. Results: Our comprehensive analysis unveiled a remarkable diversity among the circulating tumor cells (CTCs) within the Taiwanese prostate cancer tumor microenvironment. Specifically, we identified four distinct CTC clusters, each infused with different cellular components that suggest unique roles in tumor dynamics. CTC1 is comprised purely of epithelial cells, presenting a classical phenotype of circulating tumor cells, which underscores the conventional understanding of CTCs in cancer dissemination. Meanwhile, CTC2 is characterized by an infusion with N1 neutrophils, highlighting its potential role in promoting inflammatory responses that could affect tumor growth and patient prognosis. In contrast, CTC3 includes an infusion with N2 neutrophils, indicating a possible contribution to enhanced tumor progression and metastatic potential, thereby suggesting a target for therapeutic intervention to curb tumor spread. Lastly, CTC4 is infused with plasmacytoid dendritic cells, which are known for their role in immune suppression, thereby aiding the tumor in evading immune surveillance. Conclusion: This study underscores the utility of single-cell technologies in uncovering the complex cellular interactions within prostate cancer. By detailing the unique profiles of CTC subclusters and their associations with specific immune cells, our research provides novel insights into the tumor microenvironment and identifies new targets for immunotherapy. Future research will focus on validating these markers and integrating broader genomic data to refine treatment approaches and enhance patient outcomes. Citation Format: Han Hong Huynh, Tzu-Hao Chang, Shauh-Der Yeh, Chia-Ling Hsieh, Shian-Ying Sung. Advanced single-cell RNA-seq reveals complex interactions between circulating tumor cells and immune subtypes in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6269.