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Comparison of commercial exosome isolation kits for circulating exosomal microRNA profiling

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Abstract

Circulating exosomal microRNAs (miRNAs) are valuable biomarker candidates; however, information on the characterization and mutual agreement of commercial kits for circulating exosomal miRNA profiling is scarce. Here, we analyzed the advantages and weaknesses of four commonly used commercial kits for exosomal miRNA profiling and their application to the sample of serum and/or plasma, respectively. NanoSight and Western blotting were conducted to evaluate the efficiency and purity of the isolated exosomes. In our conditions, the size distribution of the isolated particles was appropriate (40–150 nm), and ExoQuick™ Exosome Precipitation Solution (EXQ) generated a relatively high yield of exosomes. Nevertheless, albumin impurity was ubiquitous for all the four kits, and Total Exosome Isolation for serum or plasma (TEI) yielded a relatively pure isolation. We further performed Illumina sequencing combined with RT-qPCR to determine the ability of these kits for miRNA profiling. There was significant correlation of the exosomal miRNA profile and specific miRNAs between kits, but with differences depending on methods. exoRNeasy Serum/Plasma Midi Kit (EXR) and EXQ performed better in the specific exosomal miRNAs recovery. Intraassay CVs for specific miRNA measurement were 0.88–3.82, 1.19–3.77, 0–2.70, and 1.23–9.11% for EXR, TEI, EXQ, and RIBO™ Exosome Isolation Reagent (REI), respectively. In each kit, serum yielded a higher abundance of exosomes and exosomal miRNAs than plasma, yet with more albumin impurity. In conclusion, our data provide some valuable guidance for the methodology of disease biomarker identification of circulation exosomal miRNAs.

Circulating exosomal microRNAs (miRNAs) are valuable biomarker candidates; however, information on the characterization and mutual agreement of commercial kits for circulating exosomal miRNA profiling is scarce. In this study, we compared four commonly used commercially available kits for exosomal miRNAsextraction and analyzed the advantages and weaknesses of each kit and their application to the sample ofserum and/or plasma

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Acknowledgements

This study was supported by grants from the National Natural Science Foundation of China (no. 81472021 and no. 81672102) and Fund of State Key Laboratory of Analytical Chemistry for Life Science (no. 5431ZZXM1601) to C. Zhang, the National Basic Research Program of China (no. 2014CB542300) to C.-Y. Zhang, the National Natural Science Foundation of China (no. 81772282 and no. 81401257) and Foundation of Jiangsu Provincial Medical Youth Talent (QNRC2016893) to C. Wang, and the Scientific Research Foundation of Graduate School of Nanjing University (no. 2016CL09) to M. Ding.

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  1. Meng Ding and Cheng Wang contributed equally to this work.

Authors and Affiliations

  1. Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), Nanjing University School of Life Sciences, Nanjing University, 305 East Zhongshan Rd., Nanjing, 210002, Jiangsu, China

    Meng Ding, Cheng Wang, Xiaolan Lu, Cuiping Zhang & Chunni Zhang

  2. State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), Nanjing University School of Life Sciences, Nanjing University, 163 Xianlin Rd., Nanjing, 210046, Jiangsu, China

    Meng Ding, Cheng Wang, Xiaolan Lu, Cuiping Zhang, Zhen Zhou, Xi Chen, Chen-Yu Zhang, Ke Zen & Chunni Zhang

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  1. Meng Ding
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Correspondence to Chen-Yu Zhang, Ke Zen or Chunni Zhang.

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The Ethics Committee of Jinling Hospital (Nanjing, China) approved the present study. Written informed consent was obtained from all participants.

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Ding, M., Wang, C., Lu, X. et al. Comparison of commercial exosome isolation kits for circulating exosomal microRNA profiling. Anal Bioanal Chem 410, 3805–3814 (2018). https://doi.org/10.1007/s00216-018-1052-4

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  • DOI: https://doi.org/10.1007/s00216-018-1052-4

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