Engineering RNA export for measurement and manipulation of living cells - Monitoring clonal population dynamics

A system for programmable export of RNA molecules from living cells would enable both non-destructive monitoring of cell dynamics and engineering of cells capable of delivering executable RNA programs to other cells. We developed genetically encoded cellular RNA exporters, inspired by viruses, that efficiently and selectively package and secrete target RNA molecules from mammalian cells within protective nanoparticles. Exporting and sequencing RNA barcodes enabled non-destructive monitoring of cell population dynamics with clonal resolution. By incorporating fusogens into the nanoparticles, we demonstrated delivery, expression, and functional activity of mRNA in recipient cells. These engineered RNA export systems thus enable measurement of cell dynamics and establish a foundation for hybrid cell and gene therapies based on cell-to-cell delivery of RNA. This BioProject contains data related to monitoring clonal population dynamics by sequencing exported RNA barcodes. More specifically, these sequencing libraries were used to 1) monitor clonal population dynamics during drug selection, and 2) characterize the accuracy, sensitivity, and reproducibility of the reporter system.

一种可实现活细胞内RNA分子可编程输出的系统，既能实现细胞动态的无损监测，也可用于改造具备向其他细胞递送可执行RNA程序能力的细胞。受病毒启发，我们开发了遗传编码的细胞RNA输出装置，可在保护性纳米颗粒（nanoparticles）中高效且选择性地包装、分泌哺乳动物细胞内的目标RNA分子。对输出的RNA条形码（RNA barcodes）进行测序，可实现具备克隆分辨率的细胞群体动态无损监测。通过将融合因子（fusogens）整合至纳米颗粒中，我们证实了该系统可向受体细胞递送信使RNA（mRNA）并实现其表达与功能活性。因此，这类经过工程改造的RNA输出系统不仅可实现细胞动态的监测，还为基于细胞间RNA递送的杂交细胞疗法与基因疗法奠定了基础。本BioProject包含通过测序输出的RNA条形码以监测克隆群体动态的相关数据。具体而言，这些测序文库（sequencing libraries）被用于两项研究：1）监测药物筛选过程中的克隆群体动态；2）表征该报告系统的准确性、灵敏度与可重复性。