Identification of exosome-like nanoparticle-derived microRNAs from 11 edible fruits and vegetables

Juan Xiao; Siyuan Feng; Xun Wang; Keren Long; Yi Luo; Yuhao Wang; Jideng Ma; Qianzi Tang; Long Jin; Xuewei Li; Mingzhou Li

doi:10.7717/peerj.5186

Identification of exosome-like nanoparticle-derived microRNAs from 11 edible fruits and vegetables

PeerJ. 2018 Jul 31:6:e5186. doi: 10.7717/peerj.5186. eCollection 2018.

Authors

Juan Xiao^#^{1

2}, Siyuan Feng^#^{1

2}, Xun Wang^#^{1

2}, Keren Long^{1

2}, Yi Luo^{1

2}, Yuhao Wang^{1

2}, Jideng Ma^{1

2}, Qianzi Tang^{1

2}, Long Jin^{1

2}, Xuewei Li^{1

2}, Mingzhou Li^{1

2}

Affiliations

¹ Sichuan Agricultural University, Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Chengdu, People's Republic of China.
² Sichuan Agricultural University, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.

^# Contributed equally.

Abstract

Edible plant-derived exosome-like nanoparticles (EPDELNs) are novel naturally occurring plant ultrastructures that are structurally similar to exosomes. Many EPDELNs have anti-inflammatory properties. MicroRNAs (miRNAs) play a critical role in mediating physiological and pathological processes in animals and plants. Although miRNAs can be selectively encapsulated in extracellular vesicles, little is known about their expression and function in EPDELNs. In this study, we isolated nanovesicles from 11 edible fruits and vegetables and subjected the corresponding EPDELN small RNA libraries to Illumina sequencing. We identified a total of 418 miRNAs-32 to 127 per species-from the 11 EPDELN samples. Target prediction and functional analyses revealed that highly expressed miRNAs were closely associated with the inflammatory response and cancer-related pathways. The 418 miRNAs could be divided into three classes according to their EPDELN distributions: 26 "frequent" miRNAs (FMs), 39 "moderately present" miRNAs (MPMs), and 353 "rare" miRNAs (RMs). FMs were represented by fewer miRNA species than RMs but had a significantly higher cumulative expression level. Taken together, our in vitro results indicate that miRNAs in EPDELNs have the potential to regulate human mRNA.

Keywords: Cross-kingdom; Exosome-like nanoparticles; Illumina sequencing; miRNA expression profile; miRNAs expression profile.

Grants and funding

This work was supported by grants from the National Natural Science Foundation of China (31472081, 31772576 and 31522055), the Application Basic Research Plan Project of Sichuan Province (2016JY0167), the Program for Innovative Research Team of Sichuan Province (2015TD0012), the Science & Technology Support Program of Sichuan (2016NYZ0042), Sichuan Province & Chinese Academy of Science & Technology Cooperation Project (2017JZ0025), the Project of Sichuan Education Department (15ZA0008 and 15ZA0003), the National Program for Support of Top-notch Young Professionals. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.