Biological networks in Parkinson’s disease: an insight into the epigenetic mechanisms associated with this disease

Abstract

Background: Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. Result: We have studied gene co-expression network obtained from a PD-specific microarray data. The co-expression network identified 11 hub genes, of which eight genes are not previously known to be associated with PD. Further study on the functionality of these eight novel hub genes revealed that these genes play important roles in several neurodegenerative diseases. Furthermore, we have studied the tissue-specific expression and histone modification patterns of the novel hub genes. Most of these genes possess several histone modification sites those are already known to be associated with neurodegenerative diseases. Regulatory network namely mTF-miRNA-gene-gTF involves microRNA Transcription Factor (mTF), microRNA (miRNA), gene and gene Transcription Factor (gTF). Whereas long noncoding RNA (lncRNA) mediated regulatory network involves miRNA, gene, mTF and lncRNA. mTF-miRNA-gene-gTF regulatory network identified a novel feed-forward loop. lncRNA-mediated regulatory network identified novel lncRNAs of PD and revealed the two-way regulatory pattern of PD-specific miRNAs where miRNAs can be regulated by both the TFs and lncRNAs. SNP analysis of the most significant genes of the co-expression network identified 20 SNPs. These SNPs are present in the 3′ UTR of known PD genes and are controlled by those miRNAs which are also involved in PD.

Retracted Article: Long noncoding RNA HOTAIR promotes cell apoptosis by sponging miR-221 in Parkinson's disease

“…The available evidence indicates the importance of biological networks of lncRNAs and miR-NAs in PD. 26 Here, we propose for the rst time that HOTAIR promotes apoptosis by sponging miR-221 in PD. A number of investigators have reported that HOTAIR exhibits pro-apoptotic roles under various conditions.…”

Long noncoding RNA and messenger RNA abnormalities in pediatric sepsis: a preliminary study

“…Then, the eligible correlated lncRNA-mRNA pairs were choosed to construct a coexpression network by Cytoscape 3.4.0 software [19]. Moreover, conservation analysis was also performed using the R package "phastCons100way.UCSC.hg19" [20][21][22].…”

SIRPα deficiency accelerates the pathologic process in models of Parkinson disease

“…The alteration of gene expression contributes to the morphological and functional change of microglia during aging (Askew et al, ; Chatterjee, Roy, Bhattacharyya, & Bandyopadhyay, ; Fonken et al, ; Soreq et al, ). It is reported that there are epigenetic changes in aged mice midbrain, which elevates the inflammatory response of microglia (Chatterjee et al, ; Phillipson, ; Tang et al, ). Primed microglia are highly sensitive, which respond to neural injury more quickly and robustly with exaggerated inflammatory response that increases neuronal vulnerability under stress conditions (Fonken et al, ; Perry & Holmes, ).…”