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Transcriptomic profiling of long non-coding RNAs in dermatomyositis by microarray analysis

View Article: PubMed Central - PubMed

ABSTRACT

Long non-coding RNAs (lncRNAs) are prevalently transcribed in the genome and have been found to be of functional importance. However, the potential roles of lncRNAs in dermatomyositis (DM) remain unknown. In this study, a lncRNA + mRNA microarray analysis was performed to profile lncRNAs and mRNAs from 15 treatment-naive DM patients and 5 healthy controls. We revealed a total of 1198 lncRNAs (322 up-regulated and 876 down-regulated) and 1213 mRNAs (665 up-regulated and 548 down-regulated) were significantly differentially expressed in DM patients compared with the healthy controls (fold change>2, P < 0.05). Subgrouping DM patients according to the presence of interstitial lung disease and anti-Jo-1 antibody revealed different expression patterns of the lncRNAs. Pathway and gene ontology analysis for the differentially expressed mRNAs confirmed that type 1 interferon signaling was the most significantly dysregulated pathway in all DM subgroups. In addition, distinct pathways that uniquely associated with DM subgroup were also identified. Bioinformatics prediction suggested that linc-DGCR6-1 may be a lncRNA that regulates type 1 interferon-inducible gene USP18, which was found highly expressed in the perifascicular areas of the muscle fibers of DM patients. Our findings provide an overview of aberrantly expressed lncRNAs in DM muscle and further broaden the understanding of DM pathogenesis.

No MeSH data available.


Comparison between the results of microarray analysis and quantitative PCR assay.Five lncRNAs (ENST00000541196.1, uc011ihb.2, linc-DGCR6-1, ENST00000551761.1, ENST00000583156.1) and five mRNAs (USP18, IFIH1, FOS, ALDH3B2, PFKFB3) were selected to be analyzed by quantitative real-time PCR to validate their expression levels relative to healthy controls. The results indicated that the microarray results correlated well with the qPCR data.
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f3: Comparison between the results of microarray analysis and quantitative PCR assay.Five lncRNAs (ENST00000541196.1, uc011ihb.2, linc-DGCR6-1, ENST00000551761.1, ENST00000583156.1) and five mRNAs (USP18, IFIH1, FOS, ALDH3B2, PFKFB3) were selected to be analyzed by quantitative real-time PCR to validate their expression levels relative to healthy controls. The results indicated that the microarray results correlated well with the qPCR data.

Mentions: Five lncRNAs and five mRNAs were selected to be analyzed by quantitative RT-PCR to validate their expression levels in the 15 DM patients involved in microarray analysis. The qRT-PCR results showed that the expression levels of lncRNAs- ENST00000541196.1, uc011ihb.2, linc-DGCR6-1, and of mRNAs- USP18, IFIH1 were significantly increased (P values all < 0.05) in DM patients compared to that in healthy controls. In addition, the expression of lncRNAs- ENST00000551761.1, ENST00000583156.1 and of mRNAs- FOS, ALDH3B2, PFKFB3 were significantly decreased (P values all < 0.05). The qRT-PCR results were consistent with the results of the microarray analysis (Fig. 3), and thus providing reliable validation for the microarray results.


Transcriptomic profiling of long non-coding RNAs in dermatomyositis by microarray analysis
Comparison between the results of microarray analysis and quantitative PCR assay.Five lncRNAs (ENST00000541196.1, uc011ihb.2, linc-DGCR6-1, ENST00000551761.1, ENST00000583156.1) and five mRNAs (USP18, IFIH1, FOS, ALDH3B2, PFKFB3) were selected to be analyzed by quantitative real-time PCR to validate their expression levels relative to healthy controls. The results indicated that the microarray results correlated well with the qPCR data.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5015085&req=5

f3: Comparison between the results of microarray analysis and quantitative PCR assay.Five lncRNAs (ENST00000541196.1, uc011ihb.2, linc-DGCR6-1, ENST00000551761.1, ENST00000583156.1) and five mRNAs (USP18, IFIH1, FOS, ALDH3B2, PFKFB3) were selected to be analyzed by quantitative real-time PCR to validate their expression levels relative to healthy controls. The results indicated that the microarray results correlated well with the qPCR data.
Mentions: Five lncRNAs and five mRNAs were selected to be analyzed by quantitative RT-PCR to validate their expression levels in the 15 DM patients involved in microarray analysis. The qRT-PCR results showed that the expression levels of lncRNAs- ENST00000541196.1, uc011ihb.2, linc-DGCR6-1, and of mRNAs- USP18, IFIH1 were significantly increased (P values all < 0.05) in DM patients compared to that in healthy controls. In addition, the expression of lncRNAs- ENST00000551761.1, ENST00000583156.1 and of mRNAs- FOS, ALDH3B2, PFKFB3 were significantly decreased (P values all < 0.05). The qRT-PCR results were consistent with the results of the microarray analysis (Fig. 3), and thus providing reliable validation for the microarray results.

View Article: PubMed Central - PubMed

ABSTRACT

Long non-coding RNAs (lncRNAs) are prevalently transcribed in the genome and have been found to be of functional importance. However, the potential roles of lncRNAs in dermatomyositis (DM) remain unknown. In this study, a lncRNA&thinsp;+&thinsp;mRNA microarray analysis was performed to profile lncRNAs and mRNAs from 15 treatment-naive DM patients and 5 healthy controls. We revealed a total of 1198 lncRNAs (322 up-regulated and 876 down-regulated) and 1213 mRNAs (665 up-regulated and 548 down-regulated) were significantly differentially expressed in DM patients compared with the healthy controls (fold change&gt;2, P&thinsp;&lt;&thinsp;0.05). Subgrouping DM patients according to the presence of interstitial lung disease and anti-Jo-1 antibody revealed different expression patterns of the lncRNAs. Pathway and gene ontology analysis for the differentially expressed mRNAs confirmed that type 1 interferon signaling was the most significantly dysregulated pathway in all DM subgroups. In addition, distinct pathways that uniquely associated with DM subgroup were also identified. Bioinformatics prediction suggested that linc-DGCR6-1 may be a lncRNA that regulates type 1 interferon-inducible gene USP18, which was found highly expressed in the perifascicular areas of the muscle fibers of DM patients. Our findings provide an overview of aberrantly expressed lncRNAs in DM muscle and further broaden the understanding of DM pathogenesis.

No MeSH data available.