Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium.
Laboratory of Molecular Angiogenesis, GIGA-Cancer, University of Liège, B34, Avenue de l'Hôpital 11, 4000, Liège, Belgium.
BMC Biol. 2022 Mar 24;20(1):72. doi: 10.1186/s12915-022-01277-4.
Extracellular vesicles (EVs) are released by nearly every cell type and have attracted much attention for their ability to transfer protein and diverse RNA species from donor to recipient cells. Much attention has been given so far to the features of EV short RNAs such as miRNAs. However, while the presence of mRNA and long noncoding RNA (lncRNA) transcripts in EVs has also been reported by multiple different groups, the properties and function of these longer transcripts have been less thoroughly explored than EV miRNA. Additionally, the impact of EV export on the transcriptome of exporting cells has remained almost completely unexamined. Here, we globally investigate mRNA and lncRNA transcripts in endothelial EVs in multiple different conditions.
In basal conditions, long RNA transcripts enriched in EVs have longer than average half-lives and distinctive stability-related sequence and structure characteristics including shorter transcript length, higher exon density, and fewer 3' UTR A/U-rich elements. EV-enriched long RNA transcripts are also enriched in HNRNPA2B1 binding motifs and are impacted by HNRNPA2B1 depletion, implicating this RNA-binding protein in the sorting of long RNA to EVs. After signaling-dependent modification of the cellular transcriptome, we observed that, unexpectedly, the rate of EV enrichment relative to cells was altered for many mRNA and lncRNA transcripts. This change in EV enrichment was negatively correlated with intracellular abundance, with transcripts whose export to EVs increased showing decreased abundance in cells and vice versa. Correspondingly, after treatment with inhibitors of EV secretion, levels of mRNA and lncRNA transcripts that are normally highly exported to EVs increased in cells, indicating a measurable impact of EV export on the long RNA transcriptome of the exporting cells. Compounds with different mechanisms of inhibition of EV secretion affected the cellular transcriptome differently, suggesting the existence of multiple EV subtypes with different long RNA profiles.
We present evidence for an impact of EV physiology on the characteristics of EV-producing cell transcriptomes. Our work suggests a new paradigm in which the sorting and packaging of transcripts into EVs participate, together with transcription and RNA decay, in controlling RNA homeostasis and shape the cellular long RNA abundance profile.
细胞外囊泡（EVs）几乎由所有细胞类型释放，并因其能够将蛋白质和多种 RNA 从供体细胞转移到受体细胞的能力而受到广泛关注。到目前为止，人们对 EV 短 RNA（如 miRNA）的特征给予了很多关注。然而，尽管多个不同的研究小组已经报道了 EV 中 mRNA 和长非编码 RNA（lncRNA）转录本的存在，但与 EV miRNA 相比，这些更长转录本的特性和功能尚未得到充分探索。此外，EV 输出对输出细胞转录组的影响几乎完全未被研究。在这里，我们在多种不同条件下对内皮细胞 EV 中的 mRNA 和 lncRNA 转录本进行了全面研究。
在基础条件下，富含 EV 的长 RNA 转录本半衰期长于平均半衰期，具有独特的稳定性相关序列和结构特征，包括较短的转录本长度、较高的外显子密度和较少的 3'UTR A/U 富含元件。EV 富集的长 RNA 转录本还富含 HNRNPA2B1 结合基序，并受 HNRNPA2B1 耗竭的影响，这表明该 RNA 结合蛋白参与了长 RNA 向 EV 的分选。在细胞转录组发生信号依赖性修饰后，我们观察到，出乎意料的是，许多 mRNA 和 lncRNA 转录本的 EV 富集率相对于细胞发生了改变。这种 EV 富集的变化与细胞内丰度呈负相关，其中向 EV 输出增加的转录本在细胞中的丰度降低，反之亦然。相应地，在用 EV 分泌抑制剂处理后，通常高度输出到 EV 的 mRNA 和 lncRNA 转录本在细胞中的水平增加，表明 EV 输出对输出细胞的长 RNA 转录组有可测量的影响。具有不同 EV 分泌抑制机制的化合物对细胞转录组的影响不同，这表明存在具有不同长 RNA 谱的多种 EV 亚型。
我们提供了 EV 生理学对 EV 产生细胞转录组特征的影响的证据。我们的工作表明了一种新的范例，其中转录本的分选和包装进入 EV 与转录和 RNA 降解一起，共同控制 RNA 内稳态并塑造细胞的长 RNA 丰度谱。
