2023,
Nature Methods.
DOI:
10.1038/s41592-023-02117-1
SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes
Ruiqiao He, Junjie Zhu, Peifeng Ji, Fangqing Zhao
Abstract:
Abstract Small extracellular vesicles (sEVs) are emerging as pivotal players in a wide range of physiological and pathological processes. However, a pressing challenge has been the lack of high-throughput techniques capable of unraveling the intricate heterogeneity of sEVs and decoding the underlying cellular behaviors governing sEV secretion. Here we leverage droplet-based single-cell RNA sequencing (scRNA-seq) and introduce an algorithm, SEVtras, to identify sEV-containing droplets and estimate the sEV secretion activity (ESAI) of individual cells. Through extensive validations on both simulated and real datasets, we demonstrate SEVtras’ efficacy in capturing sEV-containing droplets and characterizing the secretion activity of specific cell types. By applying SEVtras to four tumor scRNA-seq datasets, we further illustrate that the ESAI can serve as a potent indicator of tumor progression, particularly in the early stages. With the increasing importance and availability of scRNA-seq datasets, SEVtras holds promise in offering valuable extracellular insights into the cell heterogeneity.
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2024-01-31 23:02:00
白鸟:
#paper doi:10.1038/s41592-023-02117-1 SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes.因工作需要搜到这篇文献，
1.囊泡功能简介：胞外小囊泡（sEV）是由细胞分泌的微小囊泡，携带蛋白质、脂质和RNA等多种内容物，广泛存在于组织微环境中，充当细胞间信息交流的“信使”角色，生理病理过程中的关键参与者。
2.待解决：目前缺乏能够捕获到sEV复杂异质性和追踪sEV分泌的潜在细胞的高通量技术，需要证实检出的滴液为囊泡，
3.胞外小囊泡异质性追踪算法SEVtras：判定囊泡的算法，单细胞数据中追踪分泌囊泡的细胞来源；不同样本来源，广泛论证算法可行性；
从公共数据库中汇总胞外小囊泡关联基因集，利用最大期望算法(expectation–maximization, EM)推断单个液滴中胞外小囊泡的信号分值；
4.我的疑惑：对于细胞的身份和生物学功能研究是不容易的，囊泡的研究更甚，该算法可能需要更多的基准测试来证实；单细胞技术和囊泡是否适用；如何解析有限信息的囊泡表达谱？
问题1：判定捕获的barcode是不是为真实的囊泡--->通过SEVtras判别；
问题2：先暂不判定barcode身份（假定为真实的囊泡），基因表达谱可以分析出哪些内容？--->通过高表达基因的富集分析；