Identify Down syndrome transcriptome associations using integrative analysis of microarray database and correlation-interaction network

Min Chen,Dunjin Chen,Yanhui Liu,Jin Li,Zhengfei Lai,Xiaoshun Shi,Shuya Xue,Jiayan Wang,Yingjun Luo,Haimei Gao,Allen Chen,Kailing Huang

doi:10.1186/s40246-018-0133-y

Abstract

BackgroundLong non-coding RNAs (lncRNAs) have previously been emerged as key players in a series of biological processes. Dysregulation of lncRNA is correlated to human diseases including neurological disorders. Here, we developed a multi-step bioinformatics analysis to study the functions of a particular Down syndrome-associated gene DSCR9 including the lncRNAs. The method is named correlation-interaction-network (COIN), based on which a pipeline is implemented. Co-expression gene network analysis and biological network analysis results are presented.MethodsWe identified the regulation function of DSCR9, a lncRNA transcribed from the Down syndrome critical region (DSCR) of chromosome 21, by analyzing its co-expression genes from over 1700 sets and nearly 60,000 public Affymetrix human U133-Plus 2 transcriptional profiling microarrays. After proper evaluations, a threshold is chosen to filter the data and get satisfactory results. Microarray data resource is from EBI database and protein–protein interaction (PPI) network information is incorporated from the most complete network databases. PPI integration strategy guarantees complete information regarding DSCR9. Enrichment analysis is performed to identify significantly correlated pathways.ResultsWe found that the most significant pathways associated with the top DSCR9 co-expressed genes were shown to be involved in neuro-active ligand-receptor interaction (GLP1R, HTR4, P2RX2, UCN3, and UTS2R), calcium signaling pathway (CACNA1F, CACNG4, HTR4, P2RX2, and SLC8A3), neuronal system (KCNJ5 and SYN1) by the KEGG, and GO analysis. The A549 and U251 cell lines with stable DSCR9 overexpression were constructed. We validated 10 DSCR9 co-expression genes by qPCR in both cell lines with over 70% accuracy.ConclusionsDSCR9 was highly correlated with genes that were known as important factors in the developments and functions of nervous system, indicating that DSCR9 may regulate neurological proteins regarding Down syndrome and other neurological-related diseases. The pipeline can be properly adjusted to other applications.

Highlights

Down syndrome (DS) is the most common chromosome disorder occurring in about one per 700 newborns each year [1]
We aimed to find Long non-coding RNA (lncRNA) that are related to Down syndrome by establishing a systematic bioinformatics analysis as well as the pipeline to predict functions of lncRNAs on human chromosome 21 and by validating their potential regulatory target mRNAs by qPCR
All co-expressed probes showing high correlations with the interesting lncRNA were used for the subsequent gene ontology (GO) analysis, KEGG biological pathway analysis, and protein–protein interaction (PPI) analysis

Summary

Introduction

Down syndrome (DS) is the most common chromosome disorder occurring in about one per 700 newborns each year [1]. The involvement of DSCR as the sole cause of DS symptoms is still controversial, previous studies have suggested that this region plays a primary role in the genetic interactions related to the pathogenesis of DS. It has not been completely understood what exact subset of genes that are over-expressed on chromosome 21 generating these DSrelated deficiencies. We developed a multi-step bioinformatics analysis to study the functions of a particular Down syndrome-associated gene DSCR9 including the lncRNAs. The method is named correlation-interaction-network (COIN), based on which a pipeline is implemented. Co-expression gene network analysis and biological network analysis results are presented

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