Prediction of plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models

Qi Zhao,Tongyi Dou,Zheng Zhao,Yuanning Liu,Zhiguo Wang,Xiaoya Fan,Xiaoyu Cui,Qian Mao

doi:10.1186/s12864-018-5227-3

Abstract

BackgroundAn increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, however, some others reported negative results. Some attributed this divergence to the selective absorption of plant-derived xenomiRs by animals.ResultsHere, we analyzed 166 plant-derived xenomiRs reported in our previous study and 942 non-xenomiRs extracted from miRNA expression profiles of four species of commonly consumed plants. Employing statistics analysis and cluster analysis, our study revealed the potential sequence specificity of plant-derived xenomiRs. Furthermore, a random forest model and a one-dimensional convolutional neural network model were trained using miRNA sequence features and raw miRNA sequences respectively and then employed to predict unlabeled plant miRNAs in miRBase. A total of 241 possible plant-derived xenomiRs were predicted by both models. Finally, the potential functions of these possible plant-derived xenomiRs along with our previously reported ones in human body were analyzed.ConclusionsOur study, for the first time, presents the systematic plant-derived xenomiR sequences analysis and provides evidence for selective absorption of plant miRNA by human body, which could facilitate the future investigation about the mechanisms underlying the transference of plant-derived xenomiR.

Highlights

An increasing number of studies reported that exogenous miRNAs can be detected in animal bodies, some others reported negative results
We report the first systematic plant-derived Exogenous miRNA (xenomiR) sequences analysis, and the results provide evidence for selective absorption of plant miRNAs by human body
To obtain the non-xenomiRs as accurately as possible, we carefully selected the miRNAs that have never been detected in human from osa, Zea maize, Glycine max and Arabidopsis thaliana, which are either staple food or the plant closely related to common vegetables

Summary

Introduction

An increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, some others reported negative results. Plant-derived xenomiRs have been detected in different tissues or body fluids of several species of animals, including human [7], mice [7], pig [9], panda [10] and silkworm [11]. Their relevance to many diseases, such as cardiovascular diseases [7, 12], tumor [13, 14], chronic-inflammation [15], influenza [16], benign prostatic hyperplasia [17] and pulmonary fibrosis [18], were proposed. Many mechanisms of plant-derived xenomiRs in keeping stable in gastrointestinal (GI) track, transferring across

Methods

Results

Conclusion