Aberrantly expressed long noncoding RNAs and genes in Parkinson’s disease

Abstract

Purpose

Parkinson’s disease (PD) is a common neurodegenerative movement disorder, but the pathogenesis remains elusive. This study was aimed to explore key genes and long noncoding RNAs (lncRNAs) associated with PD.

Materials and methods

Three patients with PD and three normal controls were enrolled in the present study from July 12, 2017, to August 29, 2017. RNA sequencing and bioinformatics analysis were performed to obtain differentially expressed micro RNAs (DEmRNAs) and lncRNAs (DElncRNAs) between patients with PD and normal controls. PD-specific protein–protein interaction networks were constructed. DEmRNAs transcribed within a 100 kb window upstream or downstream of DElncRNAs were searched, which were defined as cis nearby targeted DEmRNAs of DElncRNAs. Datasets GSE57475 and GSE68719 were downloaded from the Gene Expression Omnibus database, which were used to validate the expression of selected DEmRNAs.

Results

A total of 857 DEmRNAs and 77 DElncRNAs were obtained between PD and normal controls. Natural killer cell-mediated cytotoxicity was a significantly enriched pathway in PD. ERBB2, HSPB1, and MYC were three hub proteins of PD-specific protein–protein interaction network. LOC105378701-TAL1, LOC102724104-CX3CR1, LOC105375056-TREML1/TREML4, LOC105379392-ANK1, and LOC101928100-KLRK1/KLRD1 interactions were identified DElncRNA nearby targeted DEmRNA pairs in PD. Gene expression results validated by GSE57475 and GSE68719 were consistent with our RNA-sequencing results, generally.

Conclusion

This present study identified key genes and lncRNAs associated with PD, which will provide new clues for exploring the pathogenesis and developing potential biomarkers of PD.

Keywords:

• RNA-sequencing
• mRNA
• bioinformatics analysis
• protein–protein interaction network

Acknowledgments

We thank Beijing Yangshen Bioinformatic Technology for assistance in high-throughput sequencing and data analysis. This study was supported by Nantong people’s livelihood demonstration and promotion project in 2015 (MS32015033).

Disclosure

The authors report no conflicts of interest in this work.