Limits...
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.

Show MeSH

Related in: MedlinePlus

Analysis of AK096725 mRNA expression levels from the tumor and non-tumor tissues of ccRCC patients (57 cases) and nccRCC patients (13 cases), from qRT-PCR.β-actin was used as a control. Data is shown as fold change which is the normalized expression of tumor and non-tumor tissue from the same patient. The lines are at mean with SEM. The mRNA expression of AK096725 of ccRCC patients was significantly lower than that of the nccRCC patients (P<0.001).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4048223&req=5

pone-0099372-g003: Analysis of AK096725 mRNA expression levels from the tumor and non-tumor tissues of ccRCC patients (57 cases) and nccRCC patients (13 cases), from qRT-PCR.β-actin was used as a control. Data is shown as fold change which is the normalized expression of tumor and non-tumor tissue from the same patient. The lines are at mean with SEM. The mRNA expression of AK096725 of ccRCC patients was significantly lower than that of the nccRCC patients (P<0.001).

Mentions: Interestingly, we found that the differential expression of AK096725 was likely associated with the pathogenesis of RCC, because of the difference in fold changes from normal tissues between the ccRCC (57 cases; log2FC = −1.280) and the non-clear cell RCC (nccRCC; 13 cases; log2FC = 2.381; P<0.001; Figure 3). However, the sample size of the nccRCC being limited, a further study is required to verify whether the difference is pathologically specific. This dissimilarity was not noted in the lncRNA ENST00000453068 (P = 0.132, data not shown). We also analyzed the data by stratifying samples according to pathological stage. However, no differences in expression levels were found among tumor stages for either of the two lncRNAs (P>0.05, data not shown).


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)

Analysis of AK096725 mRNA expression levels from the tumor and non-tumor tissues of ccRCC patients (57 cases) and nccRCC patients (13 cases), from qRT-PCR.β-actin was used as a control. Data is shown as fold change which is the normalized expression of tumor and non-tumor tissue from the same patient. The lines are at mean with SEM. The mRNA expression of AK096725 of ccRCC patients was significantly lower than that of the nccRCC patients (P<0.001).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0099372-g003: Analysis of AK096725 mRNA expression levels from the tumor and non-tumor tissues of ccRCC patients (57 cases) and nccRCC patients (13 cases), from qRT-PCR.β-actin was used as a control. Data is shown as fold change which is the normalized expression of tumor and non-tumor tissue from the same patient. The lines are at mean with SEM. The mRNA expression of AK096725 of ccRCC patients was significantly lower than that of the nccRCC patients (P<0.001).
Mentions: Interestingly, we found that the differential expression of AK096725 was likely associated with the pathogenesis of RCC, because of the difference in fold changes from normal tissues between the ccRCC (57 cases; log2FC = −1.280) and the non-clear cell RCC (nccRCC; 13 cases; log2FC = 2.381; P<0.001; Figure 3). However, the sample size of the nccRCC being limited, a further study is required to verify whether the difference is pathologically specific. This dissimilarity was not noted in the lncRNA ENST00000453068 (P = 0.132, data not shown). We also analyzed the data by stratifying samples according to pathological stage. However, no differences in expression levels were found among tumor stages for either of the two lncRNAs (P>0.05, data not shown).

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