LncRNAs Expression Signatures of Renal Clear Cell Carcinoma Revealed by Microarray

Yu, Guangrong; Yao, Weimin; Wang, Ji; Ma, Xin; Wu, Xiao; Li, Heng; Ding, Xia; Yang, Yang; Deng, Kangli; Xiao, Heng; Wang, Bohan; Guo, Xiaolin; Guan, Wei; Hu, Zhiquan; Bai, Yinqi; Xu, Hua; Liu, Jihong; Zhang, Xu; Ye, Zhangqun

doi:10.1371/journal.pone.0042377

Cited by 98 publications

(103 citation statements)

References 41 publications

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“…A previous study showed TRIM52-AS1 to be downregulated in RCC tissues, as determined by lncRNAs expression profiling (16,17). To confirm the result of sequencing, RT-qPCR was used to quantify the expression levels of TRIM52-AS1 in 60 matched RCC tissue samples and adjacent normal tissue samples.…”

Section: Trim52-as1 Is Downregulated In Rcc Tissues and Cell Linesmentioning

confidence: 98%

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Downregulation of long non-coding RNA TRIM52-AS1 functions as a tumor suppressor in renal cell carcinoma

Liu

Yan

Xia

et al. 2016

Molecular Medicine Reports

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Abstract. Long non-coding RNAs (lncRNAs) are important regulators of gene expression, interacting with the major pathways of cell growth, proliferation, differentiation and survival. Alterations in the function of lncRNAs promote tumor formation, progression and metastasis. The purpose of the present study was to identify novel tumor suppressor lncRNAs, and elucidate their physiological function and mechanism in renal cell carcinoma (RCC). The results of the present study revealed that the expression of the lncRNA, TRIM52-AS1, was downregulated in RCC, which was demonstrated using reverse transcription-quantitative polymerase chain reaction analysis. Furthermore, the effects of TRIM52-AS1 on proliferation, cell migration and apoptosis were analyzed using a wound scratch assay, a 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyl tetrazolium bromide assay and flow cytometric analysis, respectively. The overexpression of TRIM52-AS1 using a synthesized vector significantly suppressed cell migration and proliferation, and induced apoptosis of the RCC cells in vitro, and interference of its expression led to the opposite effects. The present study was the first, to the best of our knowledge, to demonstrate that TRIM52-AS1 functions as a tumor suppressor in RCC. Further investigation is required to elucidate the molecular mechanisms underlying the effects of TRIM52-AS1 in the development of RCC.

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Section: Trim52-as1 Is Downregulated In Rcc Tissues and Cell Linesmentioning

confidence: 98%

“…Previous sequencing for the expression of LncRNAs showed TRIM52-AS1 was downregulated in RCC (16,17). The present study was undertaken to verify the expression of TRIM52-AS1 in RCC, and to assess the impact of TRIM52-AS1 on cell proliferation, invasion and migration.…”

Section: Introductionmentioning

confidence: 94%

Downregulation of long non-coding RNA TRIM52-AS1 functions as a tumor suppressor in renal cell carcinoma

Liu

Yan

Xia

et al. 2016

Molecular Medicine Reports

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“…The differentially expressed mRNAs and lncRNAs were selected to construct the co-expression network as described in previous reports [36,37]. The network construction procedures included the following: (1) pre-processing data: for one mRNA with different transcripts, the median value was used to represent the gene expression, without special treatment for lncRNA expression values; (2) screening data: subsets of data were removed according to the lists of the differential expression of lncRNA and mRNA; (3) Pearson's correlation coefficient was calculated, and the P value was used to calculate the correlation coefficient between lncRNAs and mRNAs; and (4) screening based on Pearson's correlation coefficient: Pearson's correlation coefficients greater than 0.99 were considered meaningful and used to draw the lncRNA/mRNA co-expression network with the Cytoscape software (V2.8.3, http://www.cytoscape.org/) [38].…”

Section: Construction Of the Coding-non-coding Gene Co-expression Netmentioning

confidence: 99%

Aberrant expression of long noncoding RNAs in cumulus cells isolated from PCOS patients

Huang

Hao

Bao

et al. 2015

J Assist Reprod Genet

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Purpose To describe the long noncoding RNA (lncRNA) profiles in cumulus cells isolated from polycystic ovary syndrome (PCOS) patients by employing a microarray and in-depth bioinformatics analysis. This information will help us understand the occurrence and development of PCOS. Methods In this study, we used a microarray to describe lncRNA profiles in cumulus cells isolated from ten patients (five PCOS and five normal women). Several differentially expressed lncRNAs were chosen to validate the microarray results by quantitative RT-PCR (qRT-PCR). Then, the differentially expressed lncRNAs were classified into three subgroups (HOX loci lncRNA, enhancer-like lncRNA, and lincRNA) to deduce their potential features. Furthermore, a lncRNA/mRNA co-expression network was constructed by using the Cytoscape software (V2.8.3, http://www.cytoscape.org/). Results We observed that 623 lncRNAs and 260 messenger RNAs (mRNAs) were significantly up-or down-regulated (≥2-fold change), and these differences could be used to discriminate cumulus cells of PCOS from those of normal pat i e n t s . F i v e d i f f e r e n t i a l l y e x p r e s s e d l n c R N A s (XLOC_011402, ENST00000454271, ENST00000433673, ENST00000450294, and ENST00000432431) were selected to validate the microarray results using quantitative RT-PCR (qRT-PCR). The qRT-PCR results were consistent with the microarray data. Further analysis indicated that many differentially expressed lncRNAs were transcribed from chromosome 2 and may act as enhancers to regulate their neighboring protein-coding genes. Forty-three lncRNAs and 29 mRNAs were used to construct the coding-non-coding gene coexpression network. Most pairs positively correlated, and one mRNA correlated with one or more lncRNAs. Conclusions Our study is the first to determine genome-wide lncRNA expression patterns in cumulus cells isolated from PCOS patients by microarray. The results show that clusters of lncRNAs were aberrantly expressed in cumulus cells of PCOS patients compared with those of normal women, which revealed that lncRNAs differentially expressed in PCOS and normal women may contribute to the occurrence of PCOS and affect oocyte development.

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“…Using a range of techniques, such as microarray, 18 RNA sequencing, 19 and real-time PCR, 20 many studies have confirmed that lncRNA expression levels differ between normal and tumor tissues and vary among tumor types. [21][22][23] Although some of these abnormal expression patterns may be secondary effects from the cancer transformation, several factors suggest that lncRNAs could influence tumorigenesis. These factors include the tremendous complexity and diversity of the lncRNA landscape, the finding that lncRNAs are often located at crucial sites (eg, regions of singlenucleotide polymorphisms (SNPs), amplifications, or at common breakpoints), the presence of sequence motifs and other elements that result in specific structures, their regulation, and their functional relationships with other nucleic acids and proteins.…”

Section: Lncrnas In Cancermentioning

confidence: 99%

Long non-coding RNAs in colorectal cancer: implications for pathogenesis and clinical application

Pan

2014

Modern Pathology

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Long non-coding RNAs (lncRNAs) are a class of newly identified non-coding RNA molecules that are emerging as key regulators of tumor initiation and development. Colorectal cancer (CRC) remains a major health problem worldwide, and there remains a need to further refine the current screening approaches as well as provide tailored diagnostic and therapeutic approaches. Multiple dysregulated lncRNAs participate in tumorigenesis through a variety of molecular mechanisms, and various regulatory factors frequently contribute to the aberrant expression of lncRNAs in CRC, thereby allowing malignant transformation. Additionally, the association of dysregulated lncRNAs with specific developmental stages and clinical outcomes indicates their potential as strong diagnostic and prognostic predictors as well as therapeutic targets. Here we provide a brief overview of the known functions of CRC-associated lncRNAs, describe some potential molecular mechanisms that underlie changes in lncRNA expression in CRC, and attempt to uncover their clinical and therapeutic potential. Keywords: colorectal cancer; diagnosis; dysregulation; long non-coding RNA; prognosis High-throughput genome-scale studies have demonstrated that more than 93% of the DNA sequences in the human genome are actively transcribed. 1 However, only approximately 5-10% of the sequences are stably transcribed into mRNA or non-coding RNA (ncRNA). Genome tiling arrays have revealed that the amount of non-coding sequence is at least four times larger than the amount of coding sequence, which indicates that only 1% of the human genome is composed of protein-coding genes and the remaining 4-9% is transcribed into ncRNAs. 2 Therefore, ncRNAs constitute a very large proportion of the total RNA molecules.The function and clinical significance of short regulatory ncRNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), were elucidated first, 3 and the regulatory roles of miRNAs have been broadly recognized in almost all physiological and pathological processes in the body, including carcinogenesis. 4 For example, we previously reported that MIR95 promotes cell proliferation and targets sorting nexin 1 in human colorectal carcinoma; 5 moreover, in colorectal cancer (CRC) patients, the plasma levels of MIR29a and MIR92a are significantly upregulated and the plasma levels of MIR601 and MIR760 are significantly downregulated; thus the levels of these miRNAs have good diagnostic value for CRC screening. 6,7 According to their transcript size, ncRNAs are grouped into two major classes: (i) small ncRNAs with transcripts o200 nucleotides (nt; eg, aforementioned siRNAs and miRNAs, Piwi-interacting RNAs, and some retrotransposon-derived RNAs) and (ii) long non-coding RNAs (lncRNAs), this class includes five broad categories: sense, antisense, bidirectional, intronic, and intergenic, based on the proximity between neighboring transcripts. 8 For a time, lncRNAs was commonly defined as a proteincoding transcripts that is 4200 nt. 9 However, this definition is arbitrary and ...

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LncRNAs Expression Signatures of Renal Clear Cell Carcinoma Revealed by Microarray

Cited by 98 publications

References 41 publications

Downregulation of long non-coding RNA TRIM52-AS1 functions as a tumor suppressor in renal cell carcinoma

Downregulation of long non-coding RNA TRIM52-AS1 functions as a tumor suppressor in renal cell carcinoma

Aberrant expression of long noncoding RNAs in cumulus cells isolated from PCOS patients

Long non-coding RNAs in colorectal cancer: implications for pathogenesis and clinical application

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