1. Integrated single-cell analysis reveals distinct epigenetic-regulated cancer cell states and a heterogeneity-guided core signature in tamoxifen-resistant breast cancer.
- Author
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Fang K, Ohihoin AG, Liu T, Choppavarapu L, Nosirov B, Wang Q, Yu XZ, Kamaraju S, Leone G, and Jin VX
- Subjects
- Humans, Female, Genetic Heterogeneity, Transcriptome, Antineoplastic Agents, Hormonal pharmacology, Antineoplastic Agents, Hormonal therapeutic use, Bone Morphogenetic Protein 7 genetics, Bone Morphogenetic Protein 7 metabolism, Cell Line, Tumor, Tamoxifen pharmacology, Tamoxifen therapeutic use, Single-Cell Analysis, Breast Neoplasms genetics, Breast Neoplasms drug therapy, Breast Neoplasms pathology, Breast Neoplasms metabolism, Drug Resistance, Neoplasm genetics, Epigenesis, Genetic, Gene Expression Regulation, Neoplastic drug effects
- Abstract
Background: Inter- and intra-tumor heterogeneity is considered a significant factor contributing to the development of endocrine resistance in breast cancer. Recent advances in single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) allow us to explore inter- and intra-tumor heterogeneity at single-cell resolution. However, such integrated single-cell analysis has not yet been demonstrated to characterize the transcriptome and chromatin accessibility in breast cancer endocrine resistance., Methods: In this study, we conducted an integrated analysis combining scRNA-seq and scATAC-seq on more than 80,000 breast tissue cells from two normal tissues (NTs), three primary tumors (PTs), and three tamoxifen-treated recurrent tumors (RTs). A variety of cell types among breast tumor tissues were identified, PT- and RT-specific cancer cell states (CSs) were defined, and a heterogeneity-guided core signature (HCS) was derived through such integrated analysis. Functional experiments were performed to validate the oncogenic role of BMP7, a key gene within the core signature., Results: We observed a striking level of cell-to-cell heterogeneity among six tumor tissues and delineated the primary to recurrent tumor progression, underscoring the significance of these single-cell level tumor cell clusters classified from scRNA-seq data. We defined nine CSs, including five PT-specific, three RT-specific, and one PT-RT-shared CSs, and identified distinct open chromatin regions of CSs, as well as a HCS of 137 genes. In addition, we predicted specific transcription factors (TFs) associated with the core signature and novel biological/metabolism pathways that mediate the communications between CSs and the tumor microenvironment (TME). We finally demonstrated that BMP7 plays an oncogenic role in tamoxifen-resistant breast cancer cells through modulating MAPK signaling pathways., Conclusions: Our integrated single-cell analysis provides a comprehensive understanding of the tumor heterogeneity in tamoxifen resistance. We envision this integrated single-cell epigenomic and transcriptomic measure will become a powerful approach to unravel how epigenetic factors and the tumor microenvironment govern the development of tumor heterogeneity and to uncover potential therapeutic targets that circumvent heterogeneity-related failures., Competing Interests: Declarations Ethics approval and consent to participate This study uses previously collected breast cancer patients’ pathological specimens, or diagnostic specimens from various biospecimen resources that have already been granted local Institutional Review Board (IRB) protocol approvals. All patients’ samples are de-identified but included with some basic clinical features. We will not have any keys that may link specific Health Insurance Portability and Accountability Act (HIPAA)-defined protected health information (PHI) to specific individuals. Medical College of Wisconsin has granted this study without an IRB; therefore, ethics approval was waived in this case. This study was conducted in accordance with the ethical principles outlined in the Declaration of Helsinki. Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)
- Published
- 2024
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