Cell
Volume 177, Issue 2, 4 April 2019, Pages 446-462.e16
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Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

https://doi.org/10.1016/j.cell.2019.03.024Get rights and content
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Highlights

  • exRNA sequencing complexity and reproducibility varies across isolation methods

  • Deconvolution shows differential access to exRNA carriers by different methods

  • Performance of exRNA isolation methods vary across biofluids and RNA species

  • miRDaR enables customized selection of optimal exRNA isolation methods

Summary

Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development.

Keywords

extracellular RNA
extracellular vesicles
ribonucleoprotein
lipoprotein

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