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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.


Gene Ontology (GO) analysis of differentially expressed mRNAs in DM patients.The value of -ln (p value) was calculated to reflect the significance of GO term enrichment. The top 30 enriched GO terms of up-regulated mRNAs (A) and down-regulated mRNAs (B) are shown.
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f4: Gene Ontology (GO) analysis of differentially expressed mRNAs in DM patients.The value of -ln (p value) was calculated to reflect the significance of GO term enrichment. The top 30 enriched GO terms of up-regulated mRNAs (A) and down-regulated mRNAs (B) are shown.

Mentions: Gene Ontology (GO) is a bioinformatics initiative that seeks to better represent gene and gene product attributes, providing three structured networks of defined terms: biological process, cellular component, and molecular function. By applying GO analysis, we found that the genes corresponding to the up-regulated mRNA transcripts in DM were involved in 306 GO terms in the biological process network, 34 GO terms in the cellular component network and 11 GO terms in the molecular function network. Additionally, the genes corresponding to the down-regulated mRNAs were found to be involved in 17 GO terms in biological process, 2 GO terms in cellular component, 2 GO terms in molecular function. The top 30 significant GO terms associated with dysregulated mRNAs are shown in Fig. 4. Notably, GO clustering revealed that “type 1 interferon-mediated signaling pathway” (GO:0060337), “response to type 1 interferon” (GO:0034340) were significantly up-regulated, indicating that dysregulated type 1 interferon signaling play a role in DM pathogenesis.


Transcriptomic profiling of long non-coding RNAs in dermatomyositis by microarray analysis
Gene Ontology (GO) analysis of differentially expressed mRNAs in DM patients.The value of -ln (p value) was calculated to reflect the significance of GO term enrichment. The top 30 enriched GO terms of up-regulated mRNAs (A) and down-regulated mRNAs (B) are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Gene Ontology (GO) analysis of differentially expressed mRNAs in DM patients.The value of -ln (p value) was calculated to reflect the significance of GO term enrichment. The top 30 enriched GO terms of up-regulated mRNAs (A) and down-regulated mRNAs (B) are shown.
Mentions: Gene Ontology (GO) is a bioinformatics initiative that seeks to better represent gene and gene product attributes, providing three structured networks of defined terms: biological process, cellular component, and molecular function. By applying GO analysis, we found that the genes corresponding to the up-regulated mRNA transcripts in DM were involved in 306 GO terms in the biological process network, 34 GO terms in the cellular component network and 11 GO terms in the molecular function network. Additionally, the genes corresponding to the down-regulated mRNAs were found to be involved in 17 GO terms in biological process, 2 GO terms in cellular component, 2 GO terms in molecular function. The top 30 significant GO terms associated with dysregulated mRNAs are shown in Fig. 4. Notably, GO clustering revealed that “type 1 interferon-mediated signaling pathway” (GO:0060337), “response to type 1 interferon” (GO:0034340) were significantly up-regulated, indicating that dysregulated type 1 interferon signaling play a role in DM pathogenesis.

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.