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Updated: Jun 25, 2026
Studying Triple Negative Breast Cancer Using Orthotopic Breast Cancer Model
Published on: March 20, 2020
Single-Cell Transcriptomics in Triple-Negative Breast Cancer: Implications for Radionuclide Therapy in Precision
Xiaoxiao Xing1, Huihuan Yu2, Songliang Zhang3
1Department of Surgery, Affiliated Matern&Child Care Hospital of Nantong University, Nantong City, China.
Background:
Triple-negative breast cancer (TNBC) remains one of the most clinically challenging malignancies, characterized by aggressive behavior, high metastatic propensity, and limited therapeutic options. Conventional chemotherapy and immunotherapy have demonstrated only partial efficacy, underscoring the urgent need for novel precision oncology strategies. Radionuclide therapy, including targeted radioligand therapy and theranostic approaches, has emerged as a transformative modality in precision oncology, yet its application in TNBC is constrained by an incomplete understanding of molecular targets and tumor microenvironment heterogeneity. Single-cell RNA sequencing (scRNA-seq) provides unprecedented resolution for characterizing gene expression profiles and cellular heterogeneity within the TNBC ecosystem.
Methods:
TNBC scRNA-seq data (GSE155109) were analyzed using Scanpy for quality control, dimensionality reduction, and cluster annotation. Mendelian randomization (MR) and summary-based MR analyses were employed to identify causal associations between biomarkers, gene expression levels (CASP8, RPS23, SLC22A5, CRIPAK, EMB, CTSW), and TNBC risk. Module scoring quantified risk and protective gene activities across cellular compartments. UMAP (Uniform Manifold Approximation and Projection) and diffusion pseudotime analyses delineated transcriptional trajectories. Quantitative real-time PCR (qRT-PCR) in MCF10A, MDA-MB-231, and BT-549 cell lines validated key computational findings.
Results:
Single-cell analysis resolved 18 transcriptionally distinct clusters, reflecting the complex cellular architecture of the TNBC tumor microenvironment. Risk genes including EMB and CASP8 were preferentially expressed in endothelial-enriched cell populations, while the protective gene RPS23 was enriched in stromal compartments. Risk gene modules positively correlated with angiogenic activity, and pseudotime analysis revealed progressive risk gene activation during disease evolution. qRT-PCR confirmed significant upregulation of EMB, CASP8, CTSW, and SLC22A5 in malignant lines (p < 0.01), with concomitant RPS23 downregulation, consistent with transcriptomic data. Collectively, these molecular landscapes define putative targets for radionuclide-based theranostic strategies in precision oncology.
Conclusions:
This study systematically elucidated gene expression characteristics and cellular heterogeneity in TNBC through single-cell transcriptomics, identifying key risk and protective genes with potential theranostic relevance. The identified molecular signatures represent a roadmap for developing radionuclide therapy approaches tailored to precision oncology management of TNBC.
Insights
This study used single-cell RNA sequencing to map gene expression in triple-negative breast cancer (TNBC), identifying key risk and protective genes. These findings offer a roadmap for developing targeted radionuclide therapies for TNBC precision oncology.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Triple-negative breast cancer (TNBC) presents significant clinical challenges due to its aggressive nature and limited treatment options.
- Current therapies like chemotherapy and immunotherapy show incomplete efficacy, necessitating novel precision oncology strategies.
- Radionuclide therapy offers promise but requires a deeper understanding of TNBC's molecular targets and tumor microenvironment.
Purpose of the Study:
- To characterize gene expression profiles and cellular heterogeneity in TNBC using single-cell RNA sequencing (scRNA-seq).
- To identify key risk and protective genes within the TNBC ecosystem with potential theranostic relevance.
- To establish a foundation for developing targeted radionuclide therapies for TNBC.
Main Methods:
- Analysis of TNBC scRNA-seq data (GSE155109) using Scanpy for quality control and annotation.
- Mendelian randomization (MR) analyses to determine causal links between gene expression (CASP8, RPS23, SLC22A5, CRIPAK, EMB, CTSW) and TNBC risk.
- Module scoring, UMAP, diffusion pseudotime analysis, and qRT-PCR validation in cell lines.
Main Results:
- Single-cell analysis revealed 18 distinct TNBC clusters, highlighting tumor microenvironment complexity.
- Risk genes (EMB, CASP8) were enriched in endothelial cells, while protective gene RPS23 was found in stromal cells.
- Gene expression patterns correlated with angiogenic activity and disease progression, validated by qRT-PCR.
Conclusions:
- scRNA-seq systematically elucidated TNBC's gene expression and cellular heterogeneity.
- Key risk and protective genes with theranostic potential were identified.
- These molecular signatures provide a roadmap for radionuclide therapy in TNBC precision oncology.
