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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

Overview of the microarray signatures.(A and C) Scatter-plots showing the variations in (A) the lncRNA and (C) protein-coding mRNA expressions between the tumor and non-tumor matched pairs of tissues. The values of the X and Y axes are the averaged normalized signal values of groups of samples (log2 scaled). The green lines are fold change lines (FC = 1.5). The color of the points indicates the intensities from low (blue) to high (red). The lncRNAs or mRNAs above the top green line and below the bottom green line indicated >1.5 FC between the two groups of samples. (B and D) Volcano plots of the differentially expressed (B) lncRNAs and (D) protein-coding mRNAs. The vertical lines correspond to 1.5 FC up and down and the horizontal line represents a P-value of 0.05. The red point in the plot represents the differentially expressed lncRNAs or mRNAs with statistical significance.
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pone-0099372-g001: Overview of the microarray signatures.(A and C) Scatter-plots showing the variations in (A) the lncRNA and (C) protein-coding mRNA expressions between the tumor and non-tumor matched pairs of tissues. The values of the X and Y axes are the averaged normalized signal values of groups of samples (log2 scaled). The green lines are fold change lines (FC = 1.5). The color of the points indicates the intensities from low (blue) to high (red). The lncRNAs or mRNAs above the top green line and below the bottom green line indicated >1.5 FC between the two groups of samples. (B and D) Volcano plots of the differentially expressed (B) lncRNAs and (D) protein-coding mRNAs. The vertical lines correspond to 1.5 FC up and down and the horizontal line represents a P-value of 0.05. The red point in the plot represents the differentially expressed lncRNAs or mRNAs with statistical significance.

Mentions: We obtained an overview of the aberrant lncRNAs by analyzing the microarray data (Figure 1A, 1B; Table 2). Significantly differentiated lncRNAs were defined as those with normalized expression levels consisting of fold changes greater than 1.5 (i.e., T/N>1.5 or N/T>1.5). From five paired samples we identified hundreds of significantly differentiated lncRNAs (Table S2). In total, there were 480 upregulated lncRNAs and 417 downregulated lncRNAs found in the 5 RCC patients. Specifically, the most upregulated lncRNAs were: uc001vjj.1, ENST00000414223, BC047917, uc003erl.1, and uc009wkz.1, of which uc001vjj.1 was the highest (log2FC = 3.367). The most highly downregulated were: ENST00000507950, uc001aka.2, NR_026860, NR_024256, and BC070168, of which ENST00000507950 showed the largest downregulation (log2FC = −5.611).


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)

Overview of the microarray signatures.(A and C) Scatter-plots showing the variations in (A) the lncRNA and (C) protein-coding mRNA expressions between the tumor and non-tumor matched pairs of tissues. The values of the X and Y axes are the averaged normalized signal values of groups of samples (log2 scaled). The green lines are fold change lines (FC = 1.5). The color of the points indicates the intensities from low (blue) to high (red). The lncRNAs or mRNAs above the top green line and below the bottom green line indicated >1.5 FC between the two groups of samples. (B and D) Volcano plots of the differentially expressed (B) lncRNAs and (D) protein-coding mRNAs. The vertical lines correspond to 1.5 FC up and down and the horizontal line represents a P-value of 0.05. The red point in the plot represents the differentially expressed lncRNAs or mRNAs with statistical significance.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0099372-g001: Overview of the microarray signatures.(A and C) Scatter-plots showing the variations in (A) the lncRNA and (C) protein-coding mRNA expressions between the tumor and non-tumor matched pairs of tissues. The values of the X and Y axes are the averaged normalized signal values of groups of samples (log2 scaled). The green lines are fold change lines (FC = 1.5). The color of the points indicates the intensities from low (blue) to high (red). The lncRNAs or mRNAs above the top green line and below the bottom green line indicated >1.5 FC between the two groups of samples. (B and D) Volcano plots of the differentially expressed (B) lncRNAs and (D) protein-coding mRNAs. The vertical lines correspond to 1.5 FC up and down and the horizontal line represents a P-value of 0.05. The red point in the plot represents the differentially expressed lncRNAs or mRNAs with statistical significance.
Mentions: We obtained an overview of the aberrant lncRNAs by analyzing the microarray data (Figure 1A, 1B; Table 2). Significantly differentiated lncRNAs were defined as those with normalized expression levels consisting of fold changes greater than 1.5 (i.e., T/N>1.5 or N/T>1.5). From five paired samples we identified hundreds of significantly differentiated lncRNAs (Table S2). In total, there were 480 upregulated lncRNAs and 417 downregulated lncRNAs found in the 5 RCC patients. Specifically, the most upregulated lncRNAs were: uc001vjj.1, ENST00000414223, BC047917, uc003erl.1, and uc009wkz.1, of which uc001vjj.1 was the highest (log2FC = 3.367). The most highly downregulated were: ENST00000507950, uc001aka.2, NR_026860, NR_024256, and BC070168, of which ENST00000507950 showed the largest downregulation (log2FC = −5.611).

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