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Differential miRNA Expression in Cells and Matrix Vesicles in Vascular Smooth Muscle Cells from Rats with Kidney Disease.

Chaturvedi P, Chen NX, O'Neill K, McClintick JN, Moe SM, Janga SC - PLoS ONE (2015)

Bottom Line: The percentage of miRNA to total RNA was increased in MV compared to VSMC.We found several processes including vascular smooth muscle contraction, response to hypoxia and regulation of muscle cell differentiation to be enriched.In conclusion, our results demonstrate that miRs are concentrated in MV from calcifying VSMC, and that important functions and pathways are affected by the miRs dysregulation between calcifying VSMC and the MV they produce.

View Article: PubMed Central - PubMed

Affiliation: Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, Indiana, United States of America.

ABSTRACT
Vascular calcification is a complex process and has been associated with aging, diabetes, chronic kidney disease (CKD). Although there have been several studies that examine the role of miRNAs (miRs) in bone osteogenesis, little is known about the role of miRs in vascular calcification and their role in the pathogenesis of vascular abnormalities. Matrix vesicles (MV) are known to play in important role in initiating vascular smooth muscle cell (VSMC) calcification. In the present study, we performed miRNA microarray analysis to identify the dysregulated miRs between MV and VSMC derived from CKD rats to understand the role of post-transcriptional regulatory networks governed by these miRNAs in vascular calcification and to uncover the differential miRNA content of MV. The percentage of miRNA to total RNA was increased in MV compared to VSMC. Comparison of expression profiles of miRNA by microarray demonstrated 33 miRs to be differentially expressed with the majority (~ 57%) of them down-regulated. Target genes controlled by differentially expressed miRNAs were identified utilizing two different complementary computational approaches Miranda and Targetscan to understand the functions and pathways that may be affected due to the production of MV from calcifying VSMC thereby contributing to the regulation of genes by miRs. We found several processes including vascular smooth muscle contraction, response to hypoxia and regulation of muscle cell differentiation to be enriched. Signaling pathways identified included MAP-kinase and wnt signaling that have previously been shown to be important in vascular calcification. In conclusion, our results demonstrate that miRs are concentrated in MV from calcifying VSMC, and that important functions and pathways are affected by the miRs dysregulation between calcifying VSMC and the MV they produce. This suggests that miRs may play a very important regulatory role in vascular calcification in CKD by controlling an extensive network of post-transcriptional targets.

No MeSH data available.


Related in: MedlinePlus

Network of down-regulated miRs and the targets (genes) controlled by them.Color transition of the nodes is based on the degree (number of connections) of the nodes. Here nodes comprise both miRs and their targets. A table in the figure provides information about the nodes corresponding to the miRs. 0 represents lowest degree that is 1 and 1 corresponds to highest degree which was observed to be 262 targets in this network. Red color corresponds to the highest degree and green color corresponds to lowest degree. Network is generated using cytoscape.
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pone.0131589.g005: Network of down-regulated miRs and the targets (genes) controlled by them.Color transition of the nodes is based on the degree (number of connections) of the nodes. Here nodes comprise both miRs and their targets. A table in the figure provides information about the nodes corresponding to the miRs. 0 represents lowest degree that is 1 and 1 corresponds to highest degree which was observed to be 262 targets in this network. Red color corresponds to the highest degree and green color corresponds to lowest degree. Network is generated using cytoscape.

Mentions: Micro RNA array demonstrated that 14 miRNAs increased by 2 fold or more (defined as enriched set of miRNAs) and 19 miRNA decreased at least by 2 fold or more (depleted set) in MV compared to the calcifying VSMC from which they originate using the high stringency criteria (Fig 3). By both the computational methods (Miranda and Targetscan) we demonstrated that in the enriched set, miR-328a-star_st was found to control maximum number of targets (381) followed by miR-3562 controlling 341 putative targets. In the set of depleted miRs, we found miR-24 to control 262 target mRNAs followed by miR-324-3p which controlled 215 targets. We generated network visualizations showing the network for the two sets of miRs controlling their targets using Cytoscape [18]. Fig 4 shows a network comprising of 2572 edges with all their enriched miRs and their controlled target genes. Similarly, a total of 1933 edges comprising of 19 depleted miRs and predicted targets are shown in Fig 5. As is evident from the figure miRs 328a, 3584, 667 and 3562 were found to control a large number of targets among the enriched set of miRs while the dominant players in the depleted set included miRs 24, 199a-5p, 324-3p and 19b. Further, we obtained genes which are controlled by at-least 3 miRs either enriched or depleted. This resulted in a set of 235 genes to be controlled by at least 3 miRs. Table 1 shows the list of all the dysregulated miRs for which functions and processes they control could be confidently predicted (p-value < = 0.01). Functional enrichment was performed using David and all the functions obtained at p-value < = 0.01 and top 25% are displayed (For extended information see S2 Table).


Differential miRNA Expression in Cells and Matrix Vesicles in Vascular Smooth Muscle Cells from Rats with Kidney Disease.

Chaturvedi P, Chen NX, O'Neill K, McClintick JN, Moe SM, Janga SC - PLoS ONE (2015)

Network of down-regulated miRs and the targets (genes) controlled by them.Color transition of the nodes is based on the degree (number of connections) of the nodes. Here nodes comprise both miRs and their targets. A table in the figure provides information about the nodes corresponding to the miRs. 0 represents lowest degree that is 1 and 1 corresponds to highest degree which was observed to be 262 targets in this network. Red color corresponds to the highest degree and green color corresponds to lowest degree. Network is generated using cytoscape.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482652&req=5

pone.0131589.g005: Network of down-regulated miRs and the targets (genes) controlled by them.Color transition of the nodes is based on the degree (number of connections) of the nodes. Here nodes comprise both miRs and their targets. A table in the figure provides information about the nodes corresponding to the miRs. 0 represents lowest degree that is 1 and 1 corresponds to highest degree which was observed to be 262 targets in this network. Red color corresponds to the highest degree and green color corresponds to lowest degree. Network is generated using cytoscape.
Mentions: Micro RNA array demonstrated that 14 miRNAs increased by 2 fold or more (defined as enriched set of miRNAs) and 19 miRNA decreased at least by 2 fold or more (depleted set) in MV compared to the calcifying VSMC from which they originate using the high stringency criteria (Fig 3). By both the computational methods (Miranda and Targetscan) we demonstrated that in the enriched set, miR-328a-star_st was found to control maximum number of targets (381) followed by miR-3562 controlling 341 putative targets. In the set of depleted miRs, we found miR-24 to control 262 target mRNAs followed by miR-324-3p which controlled 215 targets. We generated network visualizations showing the network for the two sets of miRs controlling their targets using Cytoscape [18]. Fig 4 shows a network comprising of 2572 edges with all their enriched miRs and their controlled target genes. Similarly, a total of 1933 edges comprising of 19 depleted miRs and predicted targets are shown in Fig 5. As is evident from the figure miRs 328a, 3584, 667 and 3562 were found to control a large number of targets among the enriched set of miRs while the dominant players in the depleted set included miRs 24, 199a-5p, 324-3p and 19b. Further, we obtained genes which are controlled by at-least 3 miRs either enriched or depleted. This resulted in a set of 235 genes to be controlled by at least 3 miRs. Table 1 shows the list of all the dysregulated miRs for which functions and processes they control could be confidently predicted (p-value < = 0.01). Functional enrichment was performed using David and all the functions obtained at p-value < = 0.01 and top 25% are displayed (For extended information see S2 Table).

Bottom Line: The percentage of miRNA to total RNA was increased in MV compared to VSMC.We found several processes including vascular smooth muscle contraction, response to hypoxia and regulation of muscle cell differentiation to be enriched.In conclusion, our results demonstrate that miRs are concentrated in MV from calcifying VSMC, and that important functions and pathways are affected by the miRs dysregulation between calcifying VSMC and the MV they produce.

View Article: PubMed Central - PubMed

Affiliation: Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, Indiana, United States of America.

ABSTRACT
Vascular calcification is a complex process and has been associated with aging, diabetes, chronic kidney disease (CKD). Although there have been several studies that examine the role of miRNAs (miRs) in bone osteogenesis, little is known about the role of miRs in vascular calcification and their role in the pathogenesis of vascular abnormalities. Matrix vesicles (MV) are known to play in important role in initiating vascular smooth muscle cell (VSMC) calcification. In the present study, we performed miRNA microarray analysis to identify the dysregulated miRs between MV and VSMC derived from CKD rats to understand the role of post-transcriptional regulatory networks governed by these miRNAs in vascular calcification and to uncover the differential miRNA content of MV. The percentage of miRNA to total RNA was increased in MV compared to VSMC. Comparison of expression profiles of miRNA by microarray demonstrated 33 miRs to be differentially expressed with the majority (~ 57%) of them down-regulated. Target genes controlled by differentially expressed miRNAs were identified utilizing two different complementary computational approaches Miranda and Targetscan to understand the functions and pathways that may be affected due to the production of MV from calcifying VSMC thereby contributing to the regulation of genes by miRs. We found several processes including vascular smooth muscle contraction, response to hypoxia and regulation of muscle cell differentiation to be enriched. Signaling pathways identified included MAP-kinase and wnt signaling that have previously been shown to be important in vascular calcification. In conclusion, our results demonstrate that miRs are concentrated in MV from calcifying VSMC, and that important functions and pathways are affected by the miRs dysregulation between calcifying VSMC and the MV they produce. This suggests that miRs may play a very important regulatory role in vascular calcification in CKD by controlling an extensive network of post-transcriptional targets.

No MeSH data available.


Related in: MedlinePlus