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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

Distributions of the lncRNAs expression levels.That most significantly different expressed were validated by qPCR in 63 pairs of RCCC and NT samples.
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pone-0042377-g003: Distributions of the lncRNAs expression levels.That most significantly different expressed were validated by qPCR in 63 pairs of RCCC and NT samples.

Mentions: The qPCR results matched well with the data of microarray and revealed that there was variability of lncRNAs expression in these tissues (Figure 3). It was likely to provide potential way to distinguish tumor tissues and adjacent normal tissues. Although noncoding RNAs in body fluid, such as serum, urine and etc, had been identified as possible biomarkers [31], it was too early for us to utilize the four lncRNAs as the possible biomarkers in RCCC just based on the present data which will be beneficial to explore novel molecular markers in RCCC. We also found that many lncRNAs expressions were significantly correlated with hundreds of protein coding genes expressions. In theory, lncRNAs have intrinsic cis-regulatory capacity and it has been confirmed, on the other hand the cis-regulatory mechanisms of lncRNAs have been described. More and more evidences confirmed that lncRNAs can act in both cis and trans [21], [32], [33] and the precise proportion of cis regulators requires more direct experimental approaches. Recently, it have been reported that more than a thousand lncRNAs are evolutionarily conserved in mammalian genomes and thus presumably function in diverse biological processes. Some studies have demonstrated that lncRNAs are involved in transcriptional regulation and its expression can be deregulated in human cancers [26]–[29]. Another team of researchers identified a new class of lncRNAs with an enhancer-like function in various human cell lines [21]. Knockdown or low expression of these lncRNAs led to decreased expression of their neighboring protein-coding genes, including several master regulators of cellular differentiation. Our microarray displayed a portion of enhancer-like lncRNAs (Table S8). Like classical enhancers, lncRNAs are orientation independent and require a minimal promoter in their target genes to enhance their transcriptions. Although the precise molecular mechanism is yet to be defined, this group of lncRNAs illustrates that eukaryotic transcription is very tightly regulated by overlapping mechanisms. All of the examples described indicate that lncRNAs can serve as a portion markers of active regulatory pathways [14]. More about this, the lncRNAs researched here should be distinguished from transcripts that are produced at enhancer sites [34], [35], the function of which has yet to be determined.


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)

Distributions of the lncRNAs expression levels.That most significantly different expressed were validated by qPCR in 63 pairs of RCCC and NT samples.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0042377-g003: Distributions of the lncRNAs expression levels.That most significantly different expressed were validated by qPCR in 63 pairs of RCCC and NT samples.
Mentions: The qPCR results matched well with the data of microarray and revealed that there was variability of lncRNAs expression in these tissues (Figure 3). It was likely to provide potential way to distinguish tumor tissues and adjacent normal tissues. Although noncoding RNAs in body fluid, such as serum, urine and etc, had been identified as possible biomarkers [31], it was too early for us to utilize the four lncRNAs as the possible biomarkers in RCCC just based on the present data which will be beneficial to explore novel molecular markers in RCCC. We also found that many lncRNAs expressions were significantly correlated with hundreds of protein coding genes expressions. In theory, lncRNAs have intrinsic cis-regulatory capacity and it has been confirmed, on the other hand the cis-regulatory mechanisms of lncRNAs have been described. More and more evidences confirmed that lncRNAs can act in both cis and trans [21], [32], [33] and the precise proportion of cis regulators requires more direct experimental approaches. Recently, it have been reported that more than a thousand lncRNAs are evolutionarily conserved in mammalian genomes and thus presumably function in diverse biological processes. Some studies have demonstrated that lncRNAs are involved in transcriptional regulation and its expression can be deregulated in human cancers [26]–[29]. Another team of researchers identified a new class of lncRNAs with an enhancer-like function in various human cell lines [21]. Knockdown or low expression of these lncRNAs led to decreased expression of their neighboring protein-coding genes, including several master regulators of cellular differentiation. Our microarray displayed a portion of enhancer-like lncRNAs (Table S8). Like classical enhancers, lncRNAs are orientation independent and require a minimal promoter in their target genes to enhance their transcriptions. Although the precise molecular mechanism is yet to be defined, this group of lncRNAs illustrates that eukaryotic transcription is very tightly regulated by overlapping mechanisms. All of the examples described indicate that lncRNAs can serve as a portion markers of active regulatory pathways [14]. More about this, the lncRNAs researched here should be distinguished from transcripts that are produced at enhancer sites [34], [35], the function of which has yet to be determined.

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