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

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

Yong Zhou, Chengzhi Gu, Jia Li, Lianhai Zhu, Guoxiang Huang, Jie Dai, Huaiyu Huang Department of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China Purpose: Parkinson’s disease (PD) is a common neurodegenerati...

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Autores principales: Zhou Y, Gu C, Li J, Zhu L, Huang G, Dai J, Huang H
Formato: article
Lenguaje:EN
Publicado: Dove Medical Press 2018
Materias:
RNA-sequencing
mRNA
bioinformatics analysis
protein-protein interaction (PPI) network
Neurosciences. Biological psychiatry. Neuropsychiatry
RC321-571
Neurology. Diseases of the nervous system
RC346-429
Acceso en línea:https://doaj.org/article/95f331c52d994cac8e86bebf3ed1ca31
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spelling oai:doaj.org-article:95f331c52d994cac8e86bebf3ed1ca312021-12-02T00:20:32ZAberrantly expressed long noncoding RNAs and genes in Parkinson's disease1178-2021https://doaj.org/article/95f331c52d994cac8e86bebf3ed1ca312018-11-01T00:00:00Zhttps://www.dovepress.com/aberrantly-expressed-long-noncoding-rnas-and-genes-in-parkinsons-disea-peer-reviewed-article-NDThttps://doaj.org/toc/1178-2021Yong Zhou, Chengzhi Gu, Jia Li, Lianhai Zhu, Guoxiang Huang, Jie Dai, Huaiyu Huang Department of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China 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 Zhou YGu CLi JZhu LHuang GDai JHuang HDove Medical PressarticleRNA-sequencingmRNAbioinformatics analysisprotein-protein interaction (PPI) networkNeurosciences. Biological psychiatry. NeuropsychiatryRC321-571Neurology. Diseases of the nervous systemRC346-429ENNeuropsychiatric Disease and Treatment, Vol Volume 14, Pp 3219-3229 (2018)
institution DOAJ
collection DOAJ
language EN
topic RNA-sequencing
mRNA
bioinformatics analysis
protein-protein interaction (PPI) network
Neurosciences. Biological psychiatry. Neuropsychiatry
RC321-571
Neurology. Diseases of the nervous system
RC346-429
spellingShingle RNA-sequencing
mRNA
bioinformatics analysis
protein-protein interaction (PPI) network
Neurosciences. Biological psychiatry. Neuropsychiatry
RC321-571
Neurology. Diseases of the nervous system
RC346-429
Zhou Y
Gu C
Li J
Zhu L
Huang G
Dai J
Huang H
Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease
description Yong Zhou, Chengzhi Gu, Jia Li, Lianhai Zhu, Guoxiang Huang, Jie Dai, Huaiyu Huang Department of Neurology, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China 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 
format article
author Zhou Y
Gu C
Li J
Zhu L
Huang G
Dai J
Huang H
author_facet Zhou Y
Gu C
Li J
Zhu L
Huang G
Dai J
Huang H
author_sort Zhou Y
title Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease
title_short Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease
title_full Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease
title_fullStr Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease
title_full_unstemmed Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease
title_sort aberrantly expressed long noncoding rnas and genes in parkinson's disease
publisher Dove Medical Press
publishDate 2018
url https://doaj.org/article/95f331c52d994cac8e86bebf3ed1ca31
work_keys_str_mv AT zhouy aberrantlyexpressedlongnoncodingrnasandgenesinparkinson39sdisease
AT guc aberrantlyexpressedlongnoncodingrnasandgenesinparkinson39sdisease
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AT zhul aberrantlyexpressedlongnoncodingrnasandgenesinparkinson39sdisease
AT huangg aberrantlyexpressedlongnoncodingrnasandgenesinparkinson39sdisease
AT daij aberrantlyexpressedlongnoncodingrnasandgenesinparkinson39sdisease
AT huangh aberrantlyexpressedlongnoncodingrnasandgenesinparkinson39sdisease
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