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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

AK139328 is not present in mouse plasma.A) The distribution of validated plasma LncRNAs in mouse livers. B) AK139328 is not present in mouse plasma. RT-PCR assay was performed to detect the existence of LncRNAs in mouse plasma and livers. The gel images shown here were the representatives of 3 independent experiments.
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pone.0133462.g006: AK139328 is not present in mouse plasma.A) The distribution of validated plasma LncRNAs in mouse livers. B) AK139328 is not present in mouse plasma. RT-PCR assay was performed to detect the existence of LncRNAs in mouse plasma and livers. The gel images shown here were the representatives of 3 independent experiments.

Mentions: To analyze the correlation of dysregulated LncRNAs between plasma and liver, we analyzed the expression levels of 308 dysregulated plasma LncRNAs in the liver using the microarray data published in our previous study [12]. Among the 64 upregulated plasma LncRNAs, 49 LncRNAs were detected in the liver as well, but all remained unchanged (Table 1, Fig 5), and remaining 15 LncRNAs were not present in the liver in microarray analysis data (Table 1, Fig 5). Among the 244 downregulated plasma LncRNAs, 196 LncRNAs were detected in the liver, but all remained unchanged (Table 1, Fig 5), and the remaining 48 LncRNAs were not present in the liver in microarray assays (Table 1, Fig 5). Among the 10 dysregulated LncRNAs validated by real time PCR assays, AK017799, AK082383, AK042407, AK013346, AK078950 and AK017046 were present in the liver without expression change after liver IRI. In contrast, microarray failed to detect the signals of AK050787, AK159006, AK017011 and mouselincRNA0842- in the liver (Table 2) [12]. To further confirm the accuracy of microarray data, the expression of these 10 LncRNAs in the liver was analyzed by RT-PCR. The RT-PCR assays also revealed that AK050787, AK159006, AK017011 and mouselincRNA0842- are not present in the liver (Fig 6A). In our previous study, microarray assays revealed that 98 LncRNAs were dysregulated in the liver after IRI [12]. In the current study, microarray assays revealed that only 19 of these dysregulated liver LncRNAs were present in the plasma. In contrast, microarray assays failed to detect the signals of the other 79 LncRNAs in the plasma (Table 3). Among the 11 dysregulated liver LncRNAs validated by real time PCR, microarray assays in the current study revealed the existence of AK028007, NR-028310, NR-015462 and NR-036616 in the plasma, but remained unchanged. In contrast, microarray assays failed to detect the signals of AK139328, AK087277, AK029601, AK054386, AK143693, AK143294 and ENSMUST0000151138 in the plasma (Table 4). To help clarify the correlation of dysregulated LncRNAs in plasma and liver, their distribution in liver and plasma after liver IRI had been also summarized in Fig 5.


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)

AK139328 is not present in mouse plasma.A) The distribution of validated plasma LncRNAs in mouse livers. B) AK139328 is not present in mouse plasma. RT-PCR assay was performed to detect the existence of LncRNAs in mouse plasma and livers. The gel images shown here were the representatives of 3 independent experiments.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133462.g006: AK139328 is not present in mouse plasma.A) The distribution of validated plasma LncRNAs in mouse livers. B) AK139328 is not present in mouse plasma. RT-PCR assay was performed to detect the existence of LncRNAs in mouse plasma and livers. The gel images shown here were the representatives of 3 independent experiments.
Mentions: To analyze the correlation of dysregulated LncRNAs between plasma and liver, we analyzed the expression levels of 308 dysregulated plasma LncRNAs in the liver using the microarray data published in our previous study [12]. Among the 64 upregulated plasma LncRNAs, 49 LncRNAs were detected in the liver as well, but all remained unchanged (Table 1, Fig 5), and remaining 15 LncRNAs were not present in the liver in microarray analysis data (Table 1, Fig 5). Among the 244 downregulated plasma LncRNAs, 196 LncRNAs were detected in the liver, but all remained unchanged (Table 1, Fig 5), and the remaining 48 LncRNAs were not present in the liver in microarray assays (Table 1, Fig 5). Among the 10 dysregulated LncRNAs validated by real time PCR assays, AK017799, AK082383, AK042407, AK013346, AK078950 and AK017046 were present in the liver without expression change after liver IRI. In contrast, microarray failed to detect the signals of AK050787, AK159006, AK017011 and mouselincRNA0842- in the liver (Table 2) [12]. To further confirm the accuracy of microarray data, the expression of these 10 LncRNAs in the liver was analyzed by RT-PCR. The RT-PCR assays also revealed that AK050787, AK159006, AK017011 and mouselincRNA0842- are not present in the liver (Fig 6A). In our previous study, microarray assays revealed that 98 LncRNAs were dysregulated in the liver after IRI [12]. In the current study, microarray assays revealed that only 19 of these dysregulated liver LncRNAs were present in the plasma. In contrast, microarray assays failed to detect the signals of the other 79 LncRNAs in the plasma (Table 3). Among the 11 dysregulated liver LncRNAs validated by real time PCR, microarray assays in the current study revealed the existence of AK028007, NR-028310, NR-015462 and NR-036616 in the plasma, but remained unchanged. In contrast, microarray assays failed to detect the signals of AK139328, AK087277, AK029601, AK054386, AK143693, AK143294 and ENSMUST0000151138 in the plasma (Table 4). To help clarify the correlation of dysregulated LncRNAs in plasma and liver, their distribution in liver and plasma after liver IRI had been also summarized in Fig 5.

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