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Comparison Analysis of Dysregulated LncRNA Profile in Mouse Plasma and Liver after Hepatic Ischemia/Reperfusion Injury.

Chen Z, Luo Y, Yang W, Ding L, Wang J, Tu J, Geng B, Cui Q, Yang J - PLoS ONE (2015)

Bottom Line: Ten dysregulated plasma LncRNAs were validated by quantitative PCR assays, confirming the accuracy of microarray analysis result.In contrast, among the 98 dysregulated liver LncRNAs after IRI, only 19 were present in the plasma, but remained unchanged.LncRNA AK139328 had been previously reported to be upregulated in the liver after IRI, and silencing of hepatic AK139328 ameliorated liver IRI.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, 38 Xueyuan Road, Beijing, 100191, China; MOE Key Lab of Molecular Cardiovascular Science, Peking University, 38 Xueyuan Road, Beijing, 100191, China.

ABSTRACT
Long noncoding RNAs (LncRNAs) have been believed to be the major transcripts in various tissues and organs, and may play important roles in regulation of many biological processes. The current study determined the LncRNA profile in mouse plasma after liver ischemia/reperfusion injury (IRI) using microarray technology. Microarray assays revealed that 64 LncRNAs were upregulated, and 244 LncRNAs were downregulated in the plasma of liver IRI mouse. Among these dysregulated plasma LncRNAs, 59-61% were intergenic, 22-25% were antisense overlap, 8-12% were sense overlap and 6-7% were bidirectional. Ten dysregulated plasma LncRNAs were validated by quantitative PCR assays, confirming the accuracy of microarray analysis result. Comparison analysis between dysregulated plasma and liver LncRNA profile after liver IRI revealed that among the 308 dysregulated plasma LncRNAs, 245 LncRNAs were present in the liver, but remained unchanged. In contrast, among the 98 dysregulated liver LncRNAs after IRI, only 19 were present in the plasma, but remained unchanged. LncRNA AK139328 had been previously reported to be upregulated in the liver after IRI, and silencing of hepatic AK139328 ameliorated liver IRI. Both microarray and RT-PCR analyses failed to detect the presence of AK139328 in mouse plasma. In summary, the current study compared the difference between dysregulated LncRNA profile in mouse plasma and liver after liver IRI, and suggested that a group of dysregulated plasma LncRNAs have the potential of becoming novel biomarkers for evaluation of ischemic liver injury.

No MeSH data available.


Related in: MedlinePlus

Dysregulated LncRNA profile in the plasma of I/R-treated mouse.Dysregulated LncRNAs in mouse plasma were identified by microarray assays as described in the methodology section. The threshold for up-regulation was fold change≥1.5 and for down-regulation, fold change≤0.7. Increased LncRNAs was presented in panel A, whereas decreased LncRNAs presented in panel B. The detailed information of the dysregulated LncRNAs was referred to S2 and S3 Tables.
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pone.0133462.g002: Dysregulated LncRNA profile in the plasma of I/R-treated mouse.Dysregulated LncRNAs in mouse plasma were identified by microarray assays as described in the methodology section. The threshold for up-regulation was fold change≥1.5 and for down-regulation, fold change≤0.7. Increased LncRNAs was presented in panel A, whereas decreased LncRNAs presented in panel B. The detailed information of the dysregulated LncRNAs was referred to S2 and S3 Tables.

Mentions: The LncRNA profile in the plasma of mice after hepatic IRI was determined by KangChen Bio-tech (Shanghai, China) using microarray technology [12, 15, 17]. Microarray assays detected the signals of a total 10206 LncRNAs in mouse plasma (The detailed information was referred to GEO accession number: GSE60726). These plasma LncRNAs are ubiquitously distributed in all chromosomes including sex chromosomes of mouse (Fig 1). Among the plasma LncRNAs after IRI, 64 LncRNAs were upregulated (Fig 2A), whereas 244 LncRNAs were downregulated (Fig 2B) when compared with sham mice. The detailed information including name, fold of change, chromosome location, size and other characters of these dysregulated LncRNAs in mouse plasma were provided in S2 and S3 Tables. In the same tables, whether one plasma LncRNA was present in the liver or not had also been indicated in the last column in red (The detailed information regarding the LncRNA expression profile in mouse liver after IRI had been referred to the previous study [12]).


Comparison Analysis of Dysregulated LncRNA Profile in Mouse Plasma and Liver after Hepatic Ischemia/Reperfusion Injury.

Chen Z, Luo Y, Yang W, Ding L, Wang J, Tu J, Geng B, Cui Q, Yang J - PLoS ONE (2015)

Dysregulated LncRNA profile in the plasma of I/R-treated mouse.Dysregulated LncRNAs in mouse plasma were identified by microarray assays as described in the methodology section. The threshold for up-regulation was fold change≥1.5 and for down-regulation, fold change≤0.7. Increased LncRNAs was presented in panel A, whereas decreased LncRNAs presented in panel B. The detailed information of the dysregulated LncRNAs was referred to S2 and S3 Tables.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4519261&req=5

pone.0133462.g002: Dysregulated LncRNA profile in the plasma of I/R-treated mouse.Dysregulated LncRNAs in mouse plasma were identified by microarray assays as described in the methodology section. The threshold for up-regulation was fold change≥1.5 and for down-regulation, fold change≤0.7. Increased LncRNAs was presented in panel A, whereas decreased LncRNAs presented in panel B. The detailed information of the dysregulated LncRNAs was referred to S2 and S3 Tables.
Mentions: The LncRNA profile in the plasma of mice after hepatic IRI was determined by KangChen Bio-tech (Shanghai, China) using microarray technology [12, 15, 17]. Microarray assays detected the signals of a total 10206 LncRNAs in mouse plasma (The detailed information was referred to GEO accession number: GSE60726). These plasma LncRNAs are ubiquitously distributed in all chromosomes including sex chromosomes of mouse (Fig 1). Among the plasma LncRNAs after IRI, 64 LncRNAs were upregulated (Fig 2A), whereas 244 LncRNAs were downregulated (Fig 2B) when compared with sham mice. The detailed information including name, fold of change, chromosome location, size and other characters of these dysregulated LncRNAs in mouse plasma were provided in S2 and S3 Tables. In the same tables, whether one plasma LncRNA was present in the liver or not had also been indicated in the last column in red (The detailed information regarding the LncRNA expression profile in mouse liver after IRI had been referred to the previous study [12]).

Bottom Line: Ten dysregulated plasma LncRNAs were validated by quantitative PCR assays, confirming the accuracy of microarray analysis result.In contrast, among the 98 dysregulated liver LncRNAs after IRI, only 19 were present in the plasma, but remained unchanged.LncRNA AK139328 had been previously reported to be upregulated in the liver after IRI, and silencing of hepatic AK139328 ameliorated liver IRI.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, 38 Xueyuan Road, Beijing, 100191, China; MOE Key Lab of Molecular Cardiovascular Science, Peking University, 38 Xueyuan Road, Beijing, 100191, China.

ABSTRACT
Long noncoding RNAs (LncRNAs) have been believed to be the major transcripts in various tissues and organs, and may play important roles in regulation of many biological processes. The current study determined the LncRNA profile in mouse plasma after liver ischemia/reperfusion injury (IRI) using microarray technology. Microarray assays revealed that 64 LncRNAs were upregulated, and 244 LncRNAs were downregulated in the plasma of liver IRI mouse. Among these dysregulated plasma LncRNAs, 59-61% were intergenic, 22-25% were antisense overlap, 8-12% were sense overlap and 6-7% were bidirectional. Ten dysregulated plasma LncRNAs were validated by quantitative PCR assays, confirming the accuracy of microarray analysis result. Comparison analysis between dysregulated plasma and liver LncRNA profile after liver IRI revealed that among the 308 dysregulated plasma LncRNAs, 245 LncRNAs were present in the liver, but remained unchanged. In contrast, among the 98 dysregulated liver LncRNAs after IRI, only 19 were present in the plasma, but remained unchanged. LncRNA AK139328 had been previously reported to be upregulated in the liver after IRI, and silencing of hepatic AK139328 ameliorated liver IRI. Both microarray and RT-PCR analyses failed to detect the presence of AK139328 in mouse plasma. In summary, the current study compared the difference between dysregulated LncRNA profile in mouse plasma and liver after liver IRI, and suggested that a group of dysregulated plasma LncRNAs have the potential of becoming novel biomarkers for evaluation of ischemic liver injury.

No MeSH data available.


Related in: MedlinePlus