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Expression pattern of long non-coding RNAs in renal cell carcinoma revealed by microarray.

Qin C, Han Z, Qian J, Bao M, Li P, Ju X, Zhang S, Zhang L, Li S, Cao Q, Lu Q, Li J, Shao P, Meng X, Zhang W, Yin C - PLoS ONE (2014)

Bottom Line: Recent large-scale transcriptome analyses have found large numbers of transcripts, including that of long non-coding RNAs (lncRNAs), which are aberrant in various diseases, especially cancers.The lncRNA microarray revealed 27,279 lncRNAs in RCC samples, of which 480 were significantly upregulated (P<0.05; T/N>1.5) and 417 were significantly downregulated (P<0.05; N/T>1.5) compared with the matched non-tumor samples.In addition, 19,995 mRNAs were detected, of which 458 were significantly upregulated (P<0.05; T/N>1.5) and 413 were significantly downregulated (P<0.05; N/T>1.5).

View Article: PubMed Central - PubMed

Affiliation: Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.

ABSTRACT

Background: Recent large-scale transcriptome analyses have found large numbers of transcripts, including that of long non-coding RNAs (lncRNAs), which are aberrant in various diseases, especially cancers. However, it is not clear whether lncRNAs are involved specifically in renal cell carcinoma (RCC). We investigated the expression patterns of lncRNAs in five RCC tumor samples (T) relative to those of matched adjacent non-tumor tissues (N) via microarray.

Methods: A microarray with 33,045 lncRNA probes and 30,215 mRNA probes was used to identify deregulated lncRNAs in five RCC patients. Furthermore, we confirmed the relative expression levels of AK096725 and ENST00000453068 in 70 paired samples by quantitative reverse transcription polymerase chain reaction (qRT-PCR).

Results: The lncRNA microarray revealed 27,279 lncRNAs in RCC samples, of which 480 were significantly upregulated (P<0.05; T/N>1.5) and 417 were significantly downregulated (P<0.05; N/T>1.5) compared with the matched non-tumor samples. In addition, 19,995 mRNAs were detected, of which 458 were significantly upregulated (P<0.05; T/N>1.5) and 413 were significantly downregulated (P<0.05; N/T>1.5). The expression level changes of AK096725 (P = 0.043) and ENST00000453068 (P<0.001) in 70 paired samples were in accord with the microarray data.

Conclusions: The study uncovered expression patterns of lncRNAs in 5 RCC patients, as well as a number of aberrant lncRNAs and mRNAs in tumor samples compared with the non-tumor tissues. The revelation of an association between AK096725 expression and RCC is especially noteworthy. These findings may help to find new biomarkers in RCC.

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Related in: MedlinePlus

Relative expressions of AK096725 and ENST00000453068 in 70 paired RCC tumor specimens and adjacent normal tissue samples determined by qRT-PCR.The expression level of lncRNAs was normalized using β-actin as an internal control. The median in each triplicate was used to calculate the relative lncRNA concentration using the comparative ΔCt method. The lines are at mean with SEM. AK096725 was found significantly differentially upregulated in tumor specimens (P = 0.043), while ENST00000453068 was identified as significantly downregulated in tumor specimens (P<0.001).
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pone-0099372-g002: Relative expressions of AK096725 and ENST00000453068 in 70 paired RCC tumor specimens and adjacent normal tissue samples determined by qRT-PCR.The expression level of lncRNAs was normalized using β-actin as an internal control. The median in each triplicate was used to calculate the relative lncRNA concentration using the comparative ΔCt method. The lines are at mean with SEM. AK096725 was found significantly differentially upregulated in tumor specimens (P = 0.043), while ENST00000453068 was identified as significantly downregulated in tumor specimens (P<0.001).

Mentions: To choose up- and down-regulated examples of lncRNAs to verify via qRT-PCR, we took note of differentially expressed lncRNAs and associated genes that have been implicated in the pathogenesis of cancer. We chose the lncRNAs AK096725 (upregulated) and ENST00000453068 (downregulated) to confirm their differential expression levels in 70 paired RCC tissues and adjacent non-tumor tissues. Levels of AK096725 were significantly greater (P = 0.043) in RCC tissues while those of ENST00000453068 was significantly lower (P<0.001; Figure 2) compared to the non-tumor tissues. These results are consistent with the microarray data.


Expression pattern of long non-coding RNAs in renal cell carcinoma revealed by microarray.

Qin C, Han Z, Qian J, Bao M, Li P, Ju X, Zhang S, Zhang L, Li S, Cao Q, Lu Q, Li J, Shao P, Meng X, Zhang W, Yin C - PLoS ONE (2014)

Relative expressions of AK096725 and ENST00000453068 in 70 paired RCC tumor specimens and adjacent normal tissue samples determined by qRT-PCR.The expression level of lncRNAs was normalized using β-actin as an internal control. The median in each triplicate was used to calculate the relative lncRNA concentration using the comparative ΔCt method. The lines are at mean with SEM. AK096725 was found significantly differentially upregulated in tumor specimens (P = 0.043), while ENST00000453068 was identified as significantly downregulated in tumor specimens (P<0.001).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4048223&req=5

pone-0099372-g002: Relative expressions of AK096725 and ENST00000453068 in 70 paired RCC tumor specimens and adjacent normal tissue samples determined by qRT-PCR.The expression level of lncRNAs was normalized using β-actin as an internal control. The median in each triplicate was used to calculate the relative lncRNA concentration using the comparative ΔCt method. The lines are at mean with SEM. AK096725 was found significantly differentially upregulated in tumor specimens (P = 0.043), while ENST00000453068 was identified as significantly downregulated in tumor specimens (P<0.001).
Mentions: To choose up- and down-regulated examples of lncRNAs to verify via qRT-PCR, we took note of differentially expressed lncRNAs and associated genes that have been implicated in the pathogenesis of cancer. We chose the lncRNAs AK096725 (upregulated) and ENST00000453068 (downregulated) to confirm their differential expression levels in 70 paired RCC tissues and adjacent non-tumor tissues. Levels of AK096725 were significantly greater (P = 0.043) in RCC tissues while those of ENST00000453068 was significantly lower (P<0.001; Figure 2) compared to the non-tumor tissues. These results are consistent with the microarray data.

Bottom Line: Recent large-scale transcriptome analyses have found large numbers of transcripts, including that of long non-coding RNAs (lncRNAs), which are aberrant in various diseases, especially cancers.The lncRNA microarray revealed 27,279 lncRNAs in RCC samples, of which 480 were significantly upregulated (P<0.05; T/N>1.5) and 417 were significantly downregulated (P<0.05; N/T>1.5) compared with the matched non-tumor samples.In addition, 19,995 mRNAs were detected, of which 458 were significantly upregulated (P<0.05; T/N>1.5) and 413 were significantly downregulated (P<0.05; N/T>1.5).

View Article: PubMed Central - PubMed

Affiliation: Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.

ABSTRACT

Background: Recent large-scale transcriptome analyses have found large numbers of transcripts, including that of long non-coding RNAs (lncRNAs), which are aberrant in various diseases, especially cancers. However, it is not clear whether lncRNAs are involved specifically in renal cell carcinoma (RCC). We investigated the expression patterns of lncRNAs in five RCC tumor samples (T) relative to those of matched adjacent non-tumor tissues (N) via microarray.

Methods: A microarray with 33,045 lncRNA probes and 30,215 mRNA probes was used to identify deregulated lncRNAs in five RCC patients. Furthermore, we confirmed the relative expression levels of AK096725 and ENST00000453068 in 70 paired samples by quantitative reverse transcription polymerase chain reaction (qRT-PCR).

Results: The lncRNA microarray revealed 27,279 lncRNAs in RCC samples, of which 480 were significantly upregulated (P<0.05; T/N>1.5) and 417 were significantly downregulated (P<0.05; N/T>1.5) compared with the matched non-tumor samples. In addition, 19,995 mRNAs were detected, of which 458 were significantly upregulated (P<0.05; T/N>1.5) and 413 were significantly downregulated (P<0.05; N/T>1.5). The expression level changes of AK096725 (P = 0.043) and ENST00000453068 (P<0.001) in 70 paired samples were in accord with the microarray data.

Conclusions: The study uncovered expression patterns of lncRNAs in 5 RCC patients, as well as a number of aberrant lncRNAs and mRNAs in tumor samples compared with the non-tumor tissues. The revelation of an association between AK096725 expression and RCC is especially noteworthy. These findings may help to find new biomarkers in RCC.

Show MeSH
Related in: MedlinePlus