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Updated: Jun 11, 2025
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
Published on: December 9, 2016
Serial single-cell RNA sequencing unveils drug resistance and metastatic traits in stage IV breast cancer
Kazutaka Otsuji1, Yoko Takahashi1,2, Tomo Osako3
1Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan.
Abstract:
Metastasis is a complex process that remains poorly understood at the molecular levels. We profiled single-cell transcriptomic, genomic, and epigenomic changes associated with cancer cell progression, chemotherapy resistance, and metastasis from a Stage IV breast cancer patient. Pretreatment- and posttreatment-specimens from the primary tumor and distant metastases were collected for single-cell RNA sequencing and subsequent cell clustering, copy number variation (CNV) estimation, transcriptomic factor estimation, and pseudotime analyses. CNV analysis revealed that a small population of pretreatment cancer cells resisted chemotherapy and expanded. New clones including Metastatic Precursor Cells (MPCs), emerged in the posttreatment primary tumors in CNV similar to metastatic cells. MPCs exhibited expression profiles indicative of epithelial-mesenchymal transition. Comparison of MPCs with metastatic cancer cells also revealed dynamic changes in transcription factors and calcitonin pathway gene expression. These findings demonstrate the utility of single-patient clinical sample analysis for understanding tumor drug resistance, regrowth, and metastasis.
Insights
This study reveals how chemotherapy resistance and metastasis develop in Stage IV breast cancer by analyzing single cells. It identifies Metastatic Precursor Cells (MPCs) that drive tumor regrowth and spread.
Area of Science:
- Oncology
- Molecular Biology
- Genomics
Background:
- Metastasis is a complex, poorly understood process in cancer progression.
- Understanding the molecular drivers of metastasis is crucial for effective cancer treatment.
- Stage IV breast cancer presents significant challenges due to its advanced nature and metastatic potential.
Purpose of the Study:
- To profile single-cell transcriptomic, genomic, and epigenomic changes in Stage IV breast cancer.
- To investigate the molecular mechanisms underlying chemotherapy resistance and metastasis.
- To identify key cellular populations involved in cancer cell progression and spread.
Main Methods:
- Single-cell RNA sequencing of pretreatment and posttreatment primary tumor and metastatic specimens.
- Cell clustering, copy number variation (CNV) analysis, and transcription factor estimation.
- Pseudotime analysis to infer developmental trajectories and identify Metastatic Precursor Cells (MPCs).
Main Results:
- Chemotherapy-resistant cancer cells were identified and expanded from pretreatment samples.
- New clones, including Metastatic Precursor Cells (MPCs), emerged in posttreatment tumors with similar CNV to metastatic cells.
- MPCs displayed gene expression profiles indicative of epithelial-mesenchymal transition and altered transcription factor activity.
Conclusions:
- Single-patient clinical sample analysis is valuable for understanding tumor drug resistance, regrowth, and metastasis.
- Metastatic Precursor Cells (MPCs) play a critical role in breast cancer metastasis.
- Dynamic changes in transcription factors and calcitonin pathways are associated with metastasis.
