Gardner Andrea L, Jost Tyler A, Brock Amy
Department of Biomedical Engineering, The University of Texas at Austin.
bioRxiv. 2024 Jun 2:2024.05.28.596337. doi: 10.1101/2024.05.28.596337.
Intratumor heterogeneity reduces treatment efficacy and complicates our understanding of tumor progression. There is a pressing need to understand the functions of heterogeneous tumor cell subpopulations within a tumor, yet biological systems to study these processes are limited. With the advent of single-cell RNA sequencing (scRNA-seq), it has become clear that some cancer cell line models include distinct subpopulations. Heterogeneous cell lines offer a unique opportunity to study the dynamics and evolution of genetically similar cancer cell subpopulations in controlled experimental settings. 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. clusterCleaver was experimentally validated using the MDA-MB-231 and MDA-MB-436 breast cancer cell lines. ESAM and BST2/tetherin were experimentally confirmed 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 and enrichment of distinct subpopulations within cell lines which paves the way for studies on the coexistence of cancer cell subpopulations in well-defined systems.
肿瘤内异质性降低了治疗效果，并使我们对肿瘤进展的理解变得复杂。迫切需要了解肿瘤内异质肿瘤细胞亚群的功能，但用于研究这些过程的生物学系统有限。随着单细胞RNA测序（scRNA-seq）的出现，很明显一些癌细胞系模型包含不同的亚群。异质细胞系为在可控实验环境中研究基因相似的癌细胞亚群的动态和进化提供了独特的机会。在这里，我们展示了clusterCleaver，这是一个计算软件包，它使用统计距离度量来识别scRNA-seq中转录组亚群最大程度独特的候选表面标志物，这些标志物可用于荧光激活细胞分选（FACS）分离。使用MDA-MB-231和MDA-MB-436乳腺癌细胞系对clusterCleaver进行了实验验证。ESAM和BST2/ tetherin在实验中被确认为表面标志物，分别识别和分离MDA-MB-231和MDA-MB-436细胞内的主要转录组亚群。clusterCleaver是一种计算高效且经过实验验证的工作流程，用于识别和富集细胞系内不同的亚群，为在明确系统中研究癌细胞亚群的共存铺平了道路。
