Heterogeneity and plasticity in healthy and atherosclerotic vasculature explored by single-cell sequencing
Heterogeneity and plasticity in healthy and atherosclerotic vasculature explored by single-cell sequencing
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DOI：
10.1093/cvr/cvz185
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发表时间：
2019-07
影响因子：
10.8
通讯作者：
K. van Kuijk;C. Kuppe;C. Betsholtz;Michael Vanlandewijck;R. Kramann;J. Sluimer
中科院分区：
文献类型：
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作者：
K. van Kuijk;C. Kuppe;C. Betsholtz;Michael Vanlandewijck;R. Kramann;J. Sluimer
摘要细胞特征及其对疾病状态的调整由于成像、荧光报告小鼠和全基因组RNA测序的最新进展而变得更加明显。未被发现的细胞异质性和/或可塑性潜在地使实验研究和临床应用复杂化，因为源自全组织“批量”测序的标志物不能产生亚型转录组和特异性标志物。在这里，我们提出了异质性和可塑性的定义，讨论目前的知识，其在脉管系统和如何这可能是改善单细胞测序（SCS）。SCS是一种新兴技术，使研究人员能够比以往任何时候都更深入地研究不同的细胞群。细胞选择方法，例如流动辅助细胞分选，以及细胞的数量可以影响SCS方法的选择。Smart-Seq 2在少量细胞上提供完整mRNA分子的测序，而Drop-seq可以在更表面的水平上对大量细胞进行测序。SCS对健康血管系统的异质性有了更多的了解，它揭示了分区在解剖轴的基因表达谱中至关重要。在患病的血管系统中，这种异质性似乎更加突出，动脉粥样硬化中新的免疫亚群的发现就是证据。血管平滑肌细胞和间充质细胞也具有这些可塑性特征，能够上调与干细胞相关的标志物，如Sca-1或CD 34。目前的SCS研究显示了重复次数、所用细胞数量或空间信息丢失的一些限制。生物信息学工具可以在当前的数据集中提供更多的见解，利用伪时间分析或RNA速度来研究细胞分化或极化。在这篇综述中，我们讨论了使用SCS在解开异质性的血管，其目前的局限性和有前途的未来应用。
Abstract Cellular characteristics and their adjustment to a state of disease have become more evident due to recent advances in imaging, fluorescent reporter mice, and whole genome RNA sequencing. The uncovered cellular heterogeneity and/or plasticity potentially complicates experimental studies and clinical applications, as markers derived from whole tissue ‘bulk’ sequencing is unable to yield a subtype transcriptome and specific markers. Here, we propose definitions on heterogeneity and plasticity, discuss current knowledge thereof in the vasculature and how this may be improved by single-cell sequencing (SCS). SCS is emerging as an emerging technique, enabling researchers to investigate different cell populations in more depth than ever before. Cell selection methods, e.g. flow assisted cell sorting, and the quantity of cells can influence the choice of SCS method. Smart-Seq2 offers sequencing of the complete mRNA molecule on a low quantity of cells, while Drop-seq is possible on large numbers of cells on a more superficial level. SCS has given more insight in heterogeneity in healthy vasculature, where it revealed that zonation is crucial in gene expression profiles among the anatomical axis. In diseased vasculature, this heterogeneity seems even more prominent with discovery of new immune subsets in atherosclerosis as proof. Vascular smooth muscle cells and mesenchymal cells also share these plastic characteristics with the ability to up-regulate markers linked to stem cells, such as Sca-1 or CD34. Current SCS studies show some limitations to the number of replicates, quantity of cells used, or the loss of spatial information. Bioinformatical tools could give some more insight in current datasets, making use of pseudo-time analysis or RNA velocity to investigate cell differentiation or polarization. In this review, we discuss the use of SCS in unravelling heterogeneity in the vasculature, its current limitations and promising future applications.