ArticleComputational and structural biotechnology journal2020
Cellular, transcriptomic and isoform heterogeneity of breast cancer cell line revealed by full-length single-cell RNA sequencing.
Article in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 36 citations in OpenAlex.
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- Comparison of single-cell long-read and short-read transcriptome sequencing via cDNA molecule matching: quality evaluation of the MAS-ISO-seq approach.NAR genomics and bioinformatics · 2025Article
- Targeting Triple-Negative Breast Cancer: Resistance Mechanisms and Therapeutic Advancements.Cancer medicine · 2025Review
- ImageDoubler: image-based doublet identification in single-cell sequencing.Nature communications · 2025Article
- Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axis.Nature communications · 2023Article
- Genetic profiling of different phenotypic subsets of breast cancer stem cells (BCSCs) in breast cancer patients.Cancer cell international · 2022Article
- Microfluidic live tracking and transcriptomics of cancer-immune cell doublets link intercellular proximity and gene regulation.Communications biology · 2022Article
- Single-cell sequencing: a promising approach for uncovering the mechanisms of tumor metastasis.Journal of hematology & oncology · 2022Review
- Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms.PLoS computational biology · 2022Article
- Target isoforms are an overlooked challenge and opportunity in chimeric antigen receptor cell therapy.Immunotherapy advances · 2022Article
- Single-Cell Sequencing Technologies in Precision Oncology.Advances in experimental medicine and biology · 2022Review
- Expression Profile of Sphingosine Kinase 1 Isoforms in Human Cancer Tissues and Cells: Importance and Clinical Relevance of the Neglected 1b-Isoform.Journal of oncology · 2022Article
- Advances in Single-Cell Sequencing Technology and Its Applications in Triple-Negative Breast Cancer.Breast cancer (Dove Medical Press) · 2022Review
- Article
- Single-cell RNA sequencing in cancer: Applications, advances, and emerging challenges.Molecular therapy oncolytics · 2021Review
- Single-cell RNA sequencing in human lung cancer: Applications, challenges, and pathway towards personalized therapy.Journal of the Chinese Medical Association : JCMA · 2021Review
- Cancer stem cell characteristics and their potential as therapeutic targets.Medical oncology (Northwood, London, England) · 2021Review
- Single cell RNA sequencing for breast cancer: present and future.Cell death discovery · 2021Review
- Molecular subtyping and functional validation of TTK, TPX2, UBE2C, and LRP8 in sensitivity of TNBC to paclitaxel.Molecular therapy. Methods & clinical development · 2021Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Tumor heterogeneity is generated through a combination of genetic and epigenetic mechanisms, the latter of which plays an important role in the generation of stem like cells responsible for tumor formation and metastasis. Although the development of single cell transcriptomic technologies holds promise to deconvolute this complexity, a number of these techniques have limitations including drop-out and uneven coverage, which challenge the further delineation of tumor heterogeneity. We adopted deep and full-length single-cell RNA sequencing on Fluidigm's Polaris platform to reveal the cellular, transcriptomic, and isoform heterogeneity of SUM149, a triple negative breast cancer (TNBC) cell line. We first validate the quality of the TNBC sequencing data with the sequencing data from erythroleukemia K562 cell line as control. We next scrutinized well-defined marker genes for cancer stem-like cell to identify different cell populations. We then profile the isoform expression data to investigate the heterogeneity of alternative splicing patterns. Though classified as triple-negative breast cancer, the SUM149 stem cells show heterogeneous expression of marker receptors (ER, PR, and HER2) across the cells. We identified three cell populations that express patterns of stemness: epithelial-mesenchymal transition (EMT) cancer stem cells (CSCs), mesenchymal-epithelial transition (MET) CSCs and Dual-EMT-MET CSCs. These cells also manifested a high level of heterogeneity in alternative splicing patterns. For example, CSCs have shown different expression patterns of the CD44v6 exon, as well as different levels of truncated EGFR transcripts, which may suggest different potentials for proliferation and invasion among cancer stem cells. Our study identified features of the landscape of previously underestimated cellular, transcriptomic, and isoform heterogeneity of cancer stem cells in triple-negative breast cancers.
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