A Computational Framework to Infer Human Disease-Associated Long Noncoding RNAs

Liu, Ming-Xi; Chen, Xing; Chen, Geng; Cui, Qinghua; Ge, Yan

doi:10.1371/journal.pone.0084408

Cited by 109 publications

(79 citation statements)

References 49 publications

(48 reference statements)

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“…With the advance of high resolution microarray and genome wide sequencing technology, lncRNAs have recently caught increasing attention ( Ma et al, 2012;Tang et al, 2013;Liu et al, 2014). Some studies suggest that dysexpression of lncRNAs is associated with numerous diseases including cancer (Wapinski and Chang, 2011;Tang et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…This yields large numbers of ncRNAs (Consortium, 2007). Based on transcript size, regulatory ncRNAs can be further divided into two subclasses: small ncRNA (20-200nt) and long ncRNAs (lncRNAs, >200nt) ( Tano and Akimitsu, 2012;Tzadok et al, 2013;Liu et al, 2014). Some lncRNAs can execute a wide range of vital functions, for instance, gene regulation (Yang et al, 2011), splicing control (Zong et al, 2011 or X chromosome dosage compensation (Tian et al, 2010) in the cell.…”

Section: Expression and Prognostic Significance Of Lncrna Malat1 In Pmentioning

confidence: 99%

See 1 more Smart Citation

Expression and Prognostic Significance of lncRNA MALAT1 in Pancreatic Cancer Tissues

Liu¹,

Chen²,

Dang³

et al. 2014

Asian Pacific Journal of Cancer Prevention

135

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Section: Discussionmentioning

confidence: 99%

Section: Expression and Prognostic Significance Of Lncrna Malat1 In Pmentioning

confidence: 99%

Expression and Prognostic Significance of lncRNA MALAT1 in Pancreatic Cancer Tissues

Liu¹,

Chen²,

Dang³

et al. 2014

Asian Pacific Journal of Cancer Prevention

135

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“…that lncRNAs function in a number of aspects of cell biology and may aid the development of tumors (33). HOTAIR, a well-studied lncRNA, has emerged as an important regulator of carcinogenesis and metastasis, and as a potential prognostic marker (34,35).…”

Section: A B Cmentioning

confidence: 99%

Suppression of PDCD4 mediated by the long non-coding RNA HOTAIR inhibits the proliferation and invasion of glioma cells

Chen¹,

Bian²,

Zhao³

et al. 2016

Oncology Letters

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Abstract. Programmed cell death protein 4 (PDCD4) has recently been demonstrated to be implicated in translation and transcription, and the regulation of cell growth. However, the mechanisms underlying PDCD4 function in glioma cells remain to be elucidated. The current study investigated the function and regulation of PDCD4 and the results demonstrated that the expression of PDCD4 was significantly reduced in glioma cells compared with normal cells. When PDCD4 was overexpressed in glioma cells, the proliferation rate and invasive capability of the cells greatly decreased, suggesting that PDCD4 functions as a tumor suppressor in this cell type. In addition, the histone modification status of the PDCD4 gene was analyzed, and chromatin immunoprecipitation assay identified a high density of histone 3 lysine 27 trimethylation on the promoter of PDCD4, which was associated with the long non-coding RNA, homeobox transcript antisense RNA (HOTAIR). The expression of HOTAIR was significantly increased in glioma cells compared with normal cells, and it exerted its function in a polycomb repressive complex 2-dependent manner. These results may provide novel approaches to therapeutically target PDCD4 and HOTAIR in patients with gliomas. IntroductionHuman gliomas are the most prevalent malignant neoplasms of the central nervous system, with an annual incidence of ~5/100,000 worldwide (1). Despite the use of aggressive surgery in combination with chemotherapy, biological therapy and radiotherapy, gliomas continue to be therapeutically challenging (2). For patients with glioblastoma, the relative 5-year survival rate is <5% (3). Novel therapies for the treatment of glioma are warranted; recent advances in the understanding of the molecular and biological nature of this disease may facilitate the development of successful therapeutics (4).PDCD4 protein was initially determined to be overexpressed during apoptosis, which subsequently suppresses tumorigenesis (5,6). Loss of PDCD4 expression is closely associated with the progression of a number of tumors, including glioblastomas (7), and kidney, ovarian and lung cancer (8-10). Low PDCD4 expression levels correlate with poor outcomes in patients with glioblastoma multiforme (11). The frequent loss of PDCD4 in glioblastoma multiforme is partly due to epigenetic silencing secondary to 5' cytosine-phosphate-guanine island methylation (12), in addition to overexpression of microRNA (miRNA)-21, which targets PDCD4 mRNA for degradation (13). Although several studies have examined PDCD4 in glioma, the detailed molecular mechanisms underlying the role of PDCD4 in glioma remain poorly understood.Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides, which are involved in various important events, including transcriptional, epigenetic and post-transcriptional regulation (14,15). A previous study profiled the lncRNA homeobox transcript antisense RNA (HOTAIR), and the results demonstrated that HOTAIR was closely correlated with poor prognosis, molecular ...

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“…This gene cluster consists of protein-coding genes and genes for non-coding RNA, and certain HOXA lncRNAs may function as biochemical markers in several forms of cancer (13,14). HOXA11-AS was first discovered in a mouse embryonic cDNA library using a probe from the sense HOXA11 cDNA sequence (15).…”

Section: Introductionmentioning

confidence: 99%

Expression and clinicopathological significance of the lncRNA HOXA11-AS in colorectal cancer

Cai

et al. 2016

Oncology Letters

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Abstract. HOXA11 antisense RNA (HOXA11-AS) is a long non-coding RNA (lncRNA) that is important in determining cancer progression. HOXA11-AS was recently identified as a novel biomarker in lung cancer progression. However, its role in colorectal cancer (CRC) remains poorly understood. The present study aimed to analyze lncRNA HOXA11-AS expression in CRC and investigate a possible association between HOXA11-AS and clinicopathological factors. HOXA11-AS expression was examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in 84 CRC tissues and adjacent non-cancerous tissues, in addition to 3 CRC cell lines and 1 human normal colorectal cell line. The results demonstrated that HOXA11-AS expression was decreased in the CRC tissues and cell lines compared with that of the controls (P<0.05). Clinicopathological analysis indicated that low HOXA11-AS expression was significantly correlated with tumor size, advanced tumor-node-metastasis stage, lymph node metastasis and carcinoembryonic antigen level of patients with CRC (P<0.05). Furthermore, the areas under the curve (AUC) were 0.613 and 0.628 for HOXA11-AS, indicating that the lncRNA is able to distinguish CRC tissue from non-cancerous tissue, and CRC tissue with lymph node metastasis from CRC without lymph node metastasis. Therefore, HOXA11-AS may function as a potential biomarker and target for novel therapeutic strategies to treat CRC.

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A Computational Framework to Infer Human Disease-Associated Long Noncoding RNAs

Cited by 109 publications

References 49 publications

Expression and Prognostic Significance of lncRNA MALAT1 in Pancreatic Cancer Tissues

Expression and Prognostic Significance of lncRNA MALAT1 in Pancreatic Cancer Tissues

Suppression of PDCD4 mediated by the long non-coding RNA HOTAIR inhibits the proliferation and invasion of glioma cells

Expression and clinicopathological significance of the lncRNA HOXA11-AS in colorectal cancer

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