ctDNA Release Heterogeneity in Luminal Breast Cancer Revealed by Single-Cell Multi-Omics Spatial Analysis
- 1National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College
Abstract
Backgroud Breast cancer is a leading cause of cancer-related mortality, and HR+/HER2-; is the predominant subtype. Molecular pathology, including PIK3CA and ESR1 mutation, informs prognosis and treatment selection. Circulating tumor DNA (ctDNA) offers a non-invasive approach for cancer monitoring, but its clinical utility is limited by tissue plasma discordance, reflecting heterogeneous ctDNA release. The cellular and spatial determinants of this release remain poorly understood, particularly in HR+/HER2-; subtype, where heterogeneity across subclones complicates liquid biopsy interpretation. Results To identify the cellular and spatial determinants of ctDNA release, we developed scMASTER, integrating single-cell transcriptomes and mutations, spatial transcriptomics and matched tumor and plasma DNA sequencing. In ten patients with non-metastatic HR+/HER2- breast cancer, eight recurrent malignant epithelial states showed distinct ctDNA release potential. Antigen-presentation, stress, mitosis and mesenchymal-like states showed high release. PIK3CA and ESR1 mutations were linked to distinct functional states and altered ctDNA detectability. Three spatial architectures, EMT-enriched regions, intraductal luminal progenitors and avascular hypoxic zones, showed high release. Tumor-microenvironment interactions were bidirectional: anti-tumoral immunity correlated with reduced release, whereas immunomodulatory components correlated with increased release. A stratification model based on these features identified high-risk, immunosuppressed patients with poor prognosis, validated across external cohorts. Conclusions Our study establishes a single-cell spatial framework for decoding ctDNA release heterogeneity, linking tumor states, somatic mutations, spatial architecture, and immune interactions to ctDNA release. These findings provide mechanistic insights into tissue-plasma discordance, offer a biological rationale for interpreting ctDNA dynamics, refine patient risk stratification and liquid biopsy-based monitoring in HR+/HER2-; breast cancer.
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BibTeX
@misc{xu2026ctdna,
title = {{ctDNA Release Heterogeneity in Luminal Breast Cancer Revealed by Single-Cell Multi-Omics Spatial Analysis}},
author = {H. Xu and P. Pu and B. Liu and Y. Gong and J. Wu and C. Guo and H. Cao and Z. Jia and Y. Liu and Y. Huang and D. Ma and J. Li and Z. Guo and T. Shang and L. Cong and R. Zhou and Q. Ouyang and X. Wang and Y. Wang and J. Su and Y. Zhang and J. Liu},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.27.754855},
url = {https://www.biorxiv.org/content/10.64898/2026.09.27.754855v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - ctDNA Release Heterogeneity in Luminal Breast Cancer Revealed by Single-Cell Multi-Omics Spatial Analysis
AU - H. Xu
AU - P. Pu
AU - B. Liu
AU - Y. Gong
AU - J. Wu
AU - C. Guo
AU - H. Cao
AU - Z. Jia
AU - Y. Liu
AU - Y. Huang
AU - D. Ma
AU - J. Li
AU - Z. Guo
AU - T. Shang
AU - L. Cong
AU - R. Zhou
AU - Q. Ouyang
AU - X. Wang
AU - Y. Wang
AU - J. Su
AU - Y. Zhang
AU - J. Liu
PY - 2026
DA - 2026/09/27
PB - bioRxiv
DO - 10.64898/2026.09.27.754855
UR - https://www.biorxiv.org/content/10.64898/2026.09.27.754855v1
AB - Backgroud Breast cancer is a leading cause of cancer-related mortality, and HR+/HER2-; is the predominant subtype. Molecular pathology, including PIK3CA and ESR1 mutation, informs prognosis and treatment selection. Circulating tumor DNA (ctDNA) offers a non-invasive approach for cancer monitoring, but its clinical utility is limited by tissue plasma discordance, reflecting heterogeneous ctDNA release. The cellular and spatial determinants of this release remain poorly understood, particularly in HR+/HER2-; subtype, where heterogeneity across subclones complicates liquid biopsy interpretation. Results To identify the cellular and spatial determinants of ctDNA release, we developed scMASTER, integrating single-cell transcriptomes and mutations, spatial transcriptomics and matched tumor and plasma DNA sequencing. In ten patients with non-metastatic HR+/HER2- breast cancer, eight recurrent malignant epithelial states showed distinct ctDNA release potential. Antigen-presentation, stress, mitosis and mesenchymal-like states showed high release. PIK3CA and ESR1 mutations were linked to distinct functional states and altered ctDNA detectability. Three spatial architectures, EMT-enriched regions, intraductal luminal progenitors and avascular hypoxic zones, showed high release. Tumor-microenvironment interactions were bidirectional: anti-tumoral immunity correlated with reduced release, whereas immunomodulatory components correlated with increased release. A stratification model based on these features identified high-risk, immunosuppressed patients with poor prognosis, validated across external cohorts. Conclusions Our study establishes a single-cell spatial framework for decoding ctDNA release heterogeneity, linking tumor states, somatic mutations, spatial architecture, and immune interactions to ctDNA release. These findings provide mechanistic insights into tissue-plasma discordance, offer a biological rationale for interpreting ctDNA dynamics, refine patient risk stratification and liquid biopsy-based monitoring in HR+/HER2-; breast cancer.
ER -