Comprehensive profiling of extracellular RNA in HPV-induced cancers using an improved pipeline for small RNA-seq analysis.
Comprehensive profiling of extracellular RNA in HPV-induced cancers using an improved pipeline for small RNA-seq analysis.
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使用改进的管道进行小的RNA-seq分析，对HPV诱导的癌症的细胞外RNA进行了全面分析。
DOI：
10.1038/s41598-020-76623-z
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发表时间：
2020-11-10
影响因子：
4.6
通讯作者：
Wang X
中科院分区：
文献类型：
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作者：
Tong F;Andress A;Tang G;Liu P;Wang X
细胞外RNA（exRNA）由于其在细胞间通讯中的重要作用以及其作为非侵入性疾病生物标志物的潜力而引起了极大的关注。然而，目前，对于分析exRNA表达的最佳方法还没有达成共识，这导致了研究之间的显著差异。为了解决这个问题，我们建立了一个实验管道，用于全面分析从细胞培养物中分离的小exRNA。通过评估六种RNA提取方案，我们开发了一种改进的方法，用于稳健地回收囊泡结合的exRNA。利用这种方法，我们对来自14个癌细胞系的外来体（EXO）、微泡（MV）和源细胞进行了小RNA测序。与细胞相比，EXO和MV类似地富含tRNA和rRNA，但缺乏snoRNA。通过miRNA谱分析，我们鉴定了一个miRNA子集，最明显的是miR-122- 5 p，其在所有14个细胞系的EXO和MV中显著过量表达。此外，我们还鉴定了与癌症类型或人乳头瘤病毒（HPV）状态相关的EXO miRNA子集，表明它们在HPV诱导的癌症中的潜在作用。总之，我们的工作为在各种细胞系统中进一步标准化exRNA分析奠定了坚实的基础。
Extracellular RNAs (exRNAs) have attracted great attention due to their essential role in cell-to-cell communication as well as their potential as non-invasive disease biomarkers. However, at present, there is no consensus on the best method to profile exRNA expression, which leads to significant variability across studies. To address this issue, we established an experimental pipeline for comprehensive profiling of small exRNAs isolated from cell culture. By evaluating six RNA extraction protocols, we developed an improved method for robust recovery of vesicle-bound exRNAs. With this method, we performed small RNA sequencing of exosomes (EXOs), microvesicles (MVs) and source cells from 14 cancer cell lines. Compared to cells, EXOs and MVs were similarly enriched in tRNAs and rRNAs, but depleted in snoRNAs. By miRNA profiling analysis, we identified a subset of miRNAs, most noticeably miR-122-5p, that were significantly over-represented in EXOs and MVs across all 14 cell lines. In addition, we also identified a subset of EXO miRNAs associated with cancer type or human papillomavirus (HPV) status, suggesting their potential roles in HPV-induced cancers. In summary, our work has laid a solid foundation for further standardization on exRNA analysis across various cellular systems.
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影响因子：
3.2
作者：
Czernek L;Düchler M
通讯作者：
Düchler M
影响因子：
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作者：
Langmead, Ben
通讯作者：
Langmead, Ben
影响因子：
6.4
作者：
Janowska-Wieczorek, A;Wysoczynski, M;Ratajczak, MZ
通讯作者：
Ratajczak, MZ
影响因子：
19.6
作者：
Alvarez, M. Lucrecia;Khosroheidari, Mahdieh;DiStefano, Johanna K.
通讯作者：
DiStefano, Johanna K.
DOI：
10.3390/life5041638
发表时间：
2015-11-27
期刊：
Life (Basel, Switzerland)
影响因子：
--
作者：
Keam SP;Hutvagner G
通讯作者：
Hutvagner G