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Live-seq实现对单细胞的时间转录组记录
2022-08-21 22:47

瑞士联邦理工学院Bart Deplancke、Julia A. Vorholt等研究人员合作开发出Live-seq实现对单细胞的时间转录组记录。2022年8月17日,《自然》杂志在线发表了这项成果。

研究人员建立了Live-seq,一种单细胞转录组分析方法,在使用流体力显微镜提取RNA的过程中保留了细胞的活力,从而可以将细胞的基态转录组与下游的分子或表型行为联系起来。为了测试Live-seq,研究人员使用了细胞生长、功能反应和全细胞转录组读出,以证明Live-seq可以准确地将不同的细胞类型和状态分层,而不会引起重大的细胞扰动。作为一个概念证明,研究人员展示了Live-seq可以用来直接绘制细胞的轨迹,方法是对单个巨噬细胞在脂多糖(LPS)刺激前后的转录组,以及脂肪基质细胞在分化前后的转录组进行顺序分析。

此外,研究人员证明了Live-seq可以作为一个转录组记录器,通过预先记录单个巨噬细胞的转录组,随后在LPS暴露后通过延时成像进行监测。这使得无监督的、全基因组范围内的基因排名成为可能,依据是它们影响巨噬细胞LPS反应异质性的能力。并揭示了基础Nfkbia表达水平和细胞周期状态是重要的表型决定因素,研究人员通过实验验证了这一点。因此,Live-seq可以通过将单细胞转录组学(scRNA-seq)从一个端点转变为一个时间分析方法来解决广泛的生物学问题。

据悉,scRNA-seq大大推进了人们描述细胞异质性的能力。然而,scRNA-seq需要裂解细胞,这阻碍了对同一细胞的进一步分子或功能分析。

附:英文原文

Title: Live-seq enables temporal transcriptomic recording of single cells

Author: Chen, Wanze, Guillaume-Gentil, Orane, Rainer, Pernille Yde, Gbelein, Christoph G., Saelens, Wouter, Gardeux, Vincent, Klaeger, Amanda, Dainese, Riccardo, Zachara, Magda, Zambelli, Tomaso, Vorholt, Julia A., Deplancke, Bart

Issue&Volume: 2022-08-17

Abstract: Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity1. However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy2,3, thus allowing to couple a cell’s ground-state transcriptome to its downstream molecular or phenotypic behaviour. To benchmark Live-seq, we used cell growth, functional responses and whole-cell transcriptome read-outs to demonstrate that Live-seq can accurately stratify diverse cell types and states without inducing major cellular perturbations. As a proof of concept, we show that Live-seq can be used to directly map a cell’s trajectory by sequentially profiling the transcriptomes of individual macrophages before and after lipopolysaccharide (LPS) stimulation, and of adipose stromal cells pre- and post-differentiation. In addition, we demonstrate that Live-seq can function as a transcriptomic recorder by preregistering the transcriptomes of individual macrophages that were subsequently monitored by time-lapse imaging after LPS exposure. This enabled the unsupervised, genome-wide ranking of genes on the basis of their ability to affect macrophage LPS response heterogeneity, revealing basal Nfkbia expression level and cell cycle state as important phenotypic determinants, which we experimentally validated. Thus, Live-seq can address a broad range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.

DOI: 10.1038/s41586-022-05046-9

Source: https://www.nature.com/articles/s41586-022-05046-9

Nature:《自然》,创刊于1869年。隶属于施普林格·自然出版集团,最新IF:69.504
官方网址:http://www.nature.com/
投稿链接:http://www.nature.com/authors/submit_manuscript.html


本期文章:《自然》:Online/在线发表

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