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LncRNAs expression signatures of renal clear cell carcinoma revealed by microarray.

Yu G, Yao W, Wang J, Ma X, Xiao W, Li H, Xia D, Yang Y, Deng K, Xiao H, Wang B, Guo X, Guan W, Hu Z, Bai Y, Xu H, Liu J, Zhang X, Ye Z - PLoS ONE (2012)

Bottom Line: From the data we found there were thousands of lncRNAs that differentially expressed (≥ 2 fold-change) in RCCC tissues compared with NT and 916 lncRNAs differentially expressed in five or more of six RCCC samples.The four lncRNAs were aberrantly expressed in RCCC compared with matched histologically normal renal tissues.The results displayed that clusters of lncRNAs were aberrantly expressed in RCCC compared with NT samples, which revealed that lncRNAs differentially expressed in tumor tissues and normal tissues may exert a partial or key role in tumor development.

View Article: PubMed Central - PubMed

Affiliation: Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

ABSTRACT

Background: Long noncoding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. They are aberrantly expressed in many types of cancers. In this study, we described lncRNAs profiles in 6 pairs of human renal clear cell carcinoma (RCCC) and the corresponding adjacent nontumorous tissues (NT) by microarray.

Methodology/principal findings: With abundant and varied probes accounting 33,045 LncRNAs in our microarray, the number of lncRNAs that expressed at a certain level could be detected is 17157. From the data we found there were thousands of lncRNAs that differentially expressed (≥ 2 fold-change) in RCCC tissues compared with NT and 916 lncRNAs differentially expressed in five or more of six RCCC samples. Compared with NT, many lncRNAs were significantly up-regulated or down-regulated in RCCC. Our data showed that down-regulated lncRNAs were more common than up-regulated ones. ENST00000456816, X91348, BC029135, NR_024418 were evaluated by qPCR in sixty-three pairs of RCCC and NT samples. The four lncRNAs were aberrantly expressed in RCCC compared with matched histologically normal renal tissues.

Conclusions/significance: Our study is the first one to determine genome-wide lncRNAs expression patterns in RCCC by microarray. The results displayed that clusters of lncRNAs were aberrantly expressed in RCCC compared with NT samples, which revealed that lncRNAs differentially expressed in tumor tissues and normal tissues may exert a partial or key role in tumor development. Taken together, this study may provide potential targets for future treatment of RCCC and novel insights into cancer biology.

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Related in: MedlinePlus

Comparison between microarray data and qPCR result.ENST00000456816, X91348, BC029135 and NR_024418 determined to be differentially expressed in RCCC samples compared with NT samples in six patients by microarray were validated by qPCR. The heights of the columns in the chart represent the log-transformed median fold changes (T/N) in expression across the six patients for each of the four lncRNAs validated; the bars represent standard errors. The validation results of the four lncRNAs indicated that the microarray data correlated well with the qPCR results.
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pone-0042377-g002: Comparison between microarray data and qPCR result.ENST00000456816, X91348, BC029135 and NR_024418 determined to be differentially expressed in RCCC samples compared with NT samples in six patients by microarray were validated by qPCR. The heights of the columns in the chart represent the log-transformed median fold changes (T/N) in expression across the six patients for each of the four lncRNAs validated; the bars represent standard errors. The validation results of the four lncRNAs indicated that the microarray data correlated well with the qPCR results.

Mentions: In the first place, we examined the expression of these four lncRNAs (ENST00000456816, X91348, BC029135 and NR_024418) in two sets renal tissues using qPCR (Table S13). These data supported a strong consistency between the qPCR result and microarray data (Figure 2). Additionally, these four lncRNAs expression have also been analyzed in the five RCCC cell lines using qPCR (data not shown). The results demonstrated that ENST00000456816, X91348 were up-regulated and BC029135, NR_024418 were down-regulated in RCCC samples compared with NT samples. (p<0.001 for each lncRNAs) (Table S14).


LncRNAs expression signatures of renal clear cell carcinoma revealed by microarray.

Yu G, Yao W, Wang J, Ma X, Xiao W, Li H, Xia D, Yang Y, Deng K, Xiao H, Wang B, Guo X, Guan W, Hu Z, Bai Y, Xu H, Liu J, Zhang X, Ye Z - PLoS ONE (2012)

Comparison between microarray data and qPCR result.ENST00000456816, X91348, BC029135 and NR_024418 determined to be differentially expressed in RCCC samples compared with NT samples in six patients by microarray were validated by qPCR. The heights of the columns in the chart represent the log-transformed median fold changes (T/N) in expression across the six patients for each of the four lncRNAs validated; the bars represent standard errors. The validation results of the four lncRNAs indicated that the microarray data correlated well with the qPCR results.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3412851&req=5

pone-0042377-g002: Comparison between microarray data and qPCR result.ENST00000456816, X91348, BC029135 and NR_024418 determined to be differentially expressed in RCCC samples compared with NT samples in six patients by microarray were validated by qPCR. The heights of the columns in the chart represent the log-transformed median fold changes (T/N) in expression across the six patients for each of the four lncRNAs validated; the bars represent standard errors. The validation results of the four lncRNAs indicated that the microarray data correlated well with the qPCR results.
Mentions: In the first place, we examined the expression of these four lncRNAs (ENST00000456816, X91348, BC029135 and NR_024418) in two sets renal tissues using qPCR (Table S13). These data supported a strong consistency between the qPCR result and microarray data (Figure 2). Additionally, these four lncRNAs expression have also been analyzed in the five RCCC cell lines using qPCR (data not shown). The results demonstrated that ENST00000456816, X91348 were up-regulated and BC029135, NR_024418 were down-regulated in RCCC samples compared with NT samples. (p<0.001 for each lncRNAs) (Table S14).

Bottom Line: From the data we found there were thousands of lncRNAs that differentially expressed (≥ 2 fold-change) in RCCC tissues compared with NT and 916 lncRNAs differentially expressed in five or more of six RCCC samples.The four lncRNAs were aberrantly expressed in RCCC compared with matched histologically normal renal tissues.The results displayed that clusters of lncRNAs were aberrantly expressed in RCCC compared with NT samples, which revealed that lncRNAs differentially expressed in tumor tissues and normal tissues may exert a partial or key role in tumor development.

View Article: PubMed Central - PubMed

Affiliation: Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

ABSTRACT

Background: Long noncoding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. They are aberrantly expressed in many types of cancers. In this study, we described lncRNAs profiles in 6 pairs of human renal clear cell carcinoma (RCCC) and the corresponding adjacent nontumorous tissues (NT) by microarray.

Methodology/principal findings: With abundant and varied probes accounting 33,045 LncRNAs in our microarray, the number of lncRNAs that expressed at a certain level could be detected is 17157. From the data we found there were thousands of lncRNAs that differentially expressed (≥ 2 fold-change) in RCCC tissues compared with NT and 916 lncRNAs differentially expressed in five or more of six RCCC samples. Compared with NT, many lncRNAs were significantly up-regulated or down-regulated in RCCC. Our data showed that down-regulated lncRNAs were more common than up-regulated ones. ENST00000456816, X91348, BC029135, NR_024418 were evaluated by qPCR in sixty-three pairs of RCCC and NT samples. The four lncRNAs were aberrantly expressed in RCCC compared with matched histologically normal renal tissues.

Conclusions/significance: Our study is the first one to determine genome-wide lncRNAs expression patterns in RCCC by microarray. The results displayed that clusters of lncRNAs were aberrantly expressed in RCCC compared with NT samples, which revealed that lncRNAs differentially expressed in tumor tissues and normal tissues may exert a partial or key role in tumor development. Taken together, this study may provide potential targets for future treatment of RCCC and novel insights into cancer biology.

Show MeSH
Related in: MedlinePlus