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RNA-Seq Expression Analysis of Enteric Neuron Cells with Rotenone Treatment and Prediction of Regulated Pathways

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Abstract

The enteric nervous system (ENS) is involved in the initiation and development of the pathological process of Parkinson’s disease (PD). The effect of rotenone on the ENS may trigger the progression of PD through the central nervous system (CNS). In this study, we used RNA-sequencing (RNA-seq) analysis to examine differential expression genes (DEGs) and pathways induced by in vitro treatment of rotenone in the enteric nervous cells isolated from rats. We identified 45 up-regulated and 30 down-regulated genes. The functional categorization revealed that the DEGs were involved in the regulation of cell differentiation and development, response to various stimuli, and regulation of neurogenesis. In addition, the pathway and network analysis showed that the Mitogen Activated Protein Kinase (MAPK), Toll-like receptor, Wnt, and Ras signaling pathways were intensively involved in the effect of rotenone on the ENS. Additionally, the quantitative real-time polymerase chain reaction result for the selected seven DEGs matched those of the RNA-seq analysis. Our results present a significant step in the identification of DEGs and provide new insight into the progression of PD in the rotenone-induced model.

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Abbreviations

ADAMTS1:

A disintegrin and metalloprotease with thrombospondin motifs 1

ANOVA:

Analysis of variance

ATP:

Adenosine triphosphate

CCK8:

Cell counting kit-8

CNS:

Central nervous system

DEGs:

Differential expression genes

DMEM-HEPES:

Dulbecco’s modified eagle medium-2-hydroxyethyl

DMSO:

Dimethylsulphoxide

EDTA:

Ethylene diamine tetraacetic acid

ENS:

Enteric nervous system

FCS:

Fetal calf serum

FPKM:

Fragment per kilobases of transcript per million fragments mapped

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

MAPK:

Mitogen activated protein kinase

MGP:

Matrix gla protein

MPTP:

1-Methyl-4-phenyl-1,2,5,6-tetrahydropyridine

NNAT:

Neuronatin

NPY:

Neuropeptide Y

PD:

Parkinson’s disease

PNS:

Peripheral nervous system

RNA-seq:

RNA-sequencing

ROS:

Reactive oxygen species

RT-PCR:

Real-time polymerase chain reaction

SD rat:

Sprague–Dawley rat

SEM:

Standard errors of mean

SERPINE2:

Serpin peptidase inhibitor, clade E, member 2

TH:

Tyrosine hydroxylase

UGT8:

2-Hydroxyacylsphingosine 1-beta-galactosyltransferase

WISP2:

Wnt1 inducible signaling pathway protein-2

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Acknowledgements

This work was Supported by National Major Scientific and Technological Special Project for Significant New Drugs Development (2014ZX09102043-003), National Natural Science Foundation of China (No. 81371403, 81671273, 81171204, and 30772280), Shanghai Science and Technology Commission (No. 13JC1401102), the Project of Shanghai Municipal Education Commission of China (No. 14YZ046), the Projects of Shanghai Municipal Health and Family Planning Commission of China (No. 20124219 and 20134049), and the Project of Shanghai Jiao Tong University of China (No. YG2013MS22).

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    1. Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai, 200065, China

      Qiang Guan, Yanyan Jiang, Lijuan Zhao, Zhiyu Nie & Lingjing Jin

    2. Department of Neurology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China

      Xijin Wang

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    Qiang Guan and Xijin Wang have contributed equally to the manuscript.

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    Guan, Q., Wang, X., Jiang, Y. et al. RNA-Seq Expression Analysis of Enteric Neuron Cells with Rotenone Treatment and Prediction of Regulated Pathways. Neurochem Res 42, 572–582 (2017). https://doi.org/10.1007/s11064-016-2112-9

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