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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.


Related in: MedlinePlus

Expression profiles of lncRNAs and mRNAs in dermatomyositis(DM) patients and healthy controls (HC) by microarray analysis.The MA plot gives a quick overview of the distribution of the microarray gene expression data (A). The values presented in the MA plot are averaged normalized values (log2-scaled). The lncRNAs and mRNAs above the top dashed line and below the bottom dashed line are those with a >2-fold or <0.5-fold change in expression between DMs and HCs. In addition, several lncRNAs and mRNAs that mentioned in this study have been highlighted in the MA plot. Heat map and hierarchical clustering are presented to show the variation in lncRNA (B) and mRNA (C) expression between DMs and HCs. Green strip indicates high relative expression and red strip indicates low relative expression.
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f1: Expression profiles of lncRNAs and mRNAs in dermatomyositis(DM) patients and healthy controls (HC) by microarray analysis.The MA plot gives a quick overview of the distribution of the microarray gene expression data (A). The values presented in the MA plot are averaged normalized values (log2-scaled). The lncRNAs and mRNAs above the top dashed line and below the bottom dashed line are those with a >2-fold or <0.5-fold change in expression between DMs and HCs. In addition, several lncRNAs and mRNAs that mentioned in this study have been highlighted in the MA plot. Heat map and hierarchical clustering are presented to show the variation in lncRNA (B) and mRNA (C) expression between DMs and HCs. Green strip indicates high relative expression and red strip indicates low relative expression.

Mentions: Through microarray analysis, we examined the lncRNA and mRNA expression profiles in the muscle of 15 DM patients and 5 healthy controls. The MA plot is shown to reflect the overall data quality (Fig. 1A). Hierarchical clustering was performed based on the lncRNA and mRNA expression values in the microarray (Fig. 1B,C). The microarray data revealed 1213 mRNAs and 1198 lncRNAs were differentially expressed in DM patients compared with the control group. Among them, 665 mRNAs were upregulated, and 548 mRNAs were downregulated in DM patients. Regarding the lncRNAs, we found that 322 were upregulated and 876 were downregulated in DM patients. Table 1 shows the top 10 upregulated and downregulated lncRNAs. All lncRNAs and mRNAs that were aberrantly expressed with an absolute fold-change greater than 5 are listed in Supplementary datasheet 2.


Transcriptomic profiling of long non-coding RNAs in dermatomyositis by microarray analysis
Expression profiles of lncRNAs and mRNAs in dermatomyositis(DM) patients and healthy controls (HC) by microarray analysis.The MA plot gives a quick overview of the distribution of the microarray gene expression data (A). The values presented in the MA plot are averaged normalized values (log2-scaled). The lncRNAs and mRNAs above the top dashed line and below the bottom dashed line are those with a >2-fold or <0.5-fold change in expression between DMs and HCs. In addition, several lncRNAs and mRNAs that mentioned in this study have been highlighted in the MA plot. Heat map and hierarchical clustering are presented to show the variation in lncRNA (B) and mRNA (C) expression between DMs and HCs. Green strip indicates high relative expression and red strip indicates low relative expression.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Expression profiles of lncRNAs and mRNAs in dermatomyositis(DM) patients and healthy controls (HC) by microarray analysis.The MA plot gives a quick overview of the distribution of the microarray gene expression data (A). The values presented in the MA plot are averaged normalized values (log2-scaled). The lncRNAs and mRNAs above the top dashed line and below the bottom dashed line are those with a >2-fold or <0.5-fold change in expression between DMs and HCs. In addition, several lncRNAs and mRNAs that mentioned in this study have been highlighted in the MA plot. Heat map and hierarchical clustering are presented to show the variation in lncRNA (B) and mRNA (C) expression between DMs and HCs. Green strip indicates high relative expression and red strip indicates low relative expression.
Mentions: Through microarray analysis, we examined the lncRNA and mRNA expression profiles in the muscle of 15 DM patients and 5 healthy controls. The MA plot is shown to reflect the overall data quality (Fig. 1A). Hierarchical clustering was performed based on the lncRNA and mRNA expression values in the microarray (Fig. 1B,C). The microarray data revealed 1213 mRNAs and 1198 lncRNAs were differentially expressed in DM patients compared with the control group. Among them, 665 mRNAs were upregulated, and 548 mRNAs were downregulated in DM patients. Regarding the lncRNAs, we found that 322 were upregulated and 876 were downregulated in DM patients. Table 1 shows the top 10 upregulated and downregulated lncRNAs. All lncRNAs and mRNAs that were aberrantly expressed with an absolute fold-change greater than 5 are listed in Supplementary datasheet 2.

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.


Related in: MedlinePlus