ArticleNPJ systems biology and applications2024
Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations.
Article in NPJ systems biology and applications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Deep learning identifies heterogeneous subpopulations in breast cancer cell lines.npj biomedical innovations · 2025Article
- Mapping cell-cell fusion at single-cell resolution.bioRxiv : the preprint server for biology · 2025Article
- 3D Culture of MSCs for Clinical Application.Bioengineering (Basel, Switzerland) · 2024Review
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Abstract
Intratumor heterogeneity reduces treatment efficacy and complicates our understanding of tumor progression and there is a pressing need to understand the functions of heterogeneous tumor cell subpopulations within a tumor, yet systems to study these processes in vitro are limited. Single-cell RNA sequencing (scRNA-seq) has revealed that some cancer cell lines include distinct subpopulations. Here, we present clusterCleaver, a computational package that uses metrics of statistical distance to identify candidate surface markers maximally unique to transcriptomic subpopulations in scRNA-seq which may be used for FACS isolation. With clusterCleaver, ESAM and BST2/tetherin were experimentally validated as surface markers which identify and separate major transcriptomic subpopulations within MDA-MB-231 and MDA-MB-436 cells, respectively. clusterCleaver is a computationally efficient and experimentally validated workflow for identification of surface markers for tracking and isolating transcriptomically distinct subpopulations within cell lines. This tool paves the way for studies on coexisting cancer cell subpopulations in well-defined in vitro systems.
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