RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings

Ren, Shancheng; Peng, Zhiyu; Mao, Jianhua; Ye, Yu; Chen, Yin; Gao, Xin; Cui, Zilian; Zhang, Jibin; Yi, Kechu; Xu, Weidong; Chen, Chao; Wang, Fubo; Guo, Xinwu; J, Lu; Yang, Jing; Wei, Min; Tian, Zhijian; Guan, Y. H.; Tang, Liang; Xu, Chuanliang; Wang, Linhui; Gao, Xu; Tian, Wenxi; Wang, Jian; Yang, Huanming; Wang, Jun; Sun, Yinghao

doi:10.1038/cr.2013.61

Cited by 43 publications

(59 citation statements)

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“…The rationale is that lncRNAs have a regulatory role in the transcription of many protein coding genes (Wang et al 2008b;Tsai et al 2010;Bi et al 2013) and many co-expressed genes are found related in function such as involved in the same signal transduction pathway. Consistent with Ren et al (2012), most of the co-expression pairs in this study displayed positive correlation suggesting an enhancer-like role of these lncRNAs in regulating the transcription of the protein coding genes. Only two co-expression pairs were presented as negative correlation including one lncRNA LINC01093 correlated with TTK and NDC80.…”

Section: Discussionsupporting

confidence: 80%

Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets

Zhang

Liu²,

Zhang

et al. 2015

Mol Genet Genomics

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Hepatocellular carcinoma (HCC) is an aggressive and deadly cancer. The molecular pathogenesis of the disease remains poorly understood. To better understand HCC biology and explore potential biomarkers and therapeutic targets, we investigated the whole transcriptome of HCC. Considering the genetic heterogeneity of HCC, four datasets from four studies consisting of 15 pairs of HCC and adjacent normal samples were analyzed. We observed that the number of lncRNAs expressed in each HCC sample was consistently greater than the adjacent normal sample. Moreover, 15 lncRNAs were identified expressed in five to seven HCC tissues but were not detected in any adjacent normal tissue. Differential expression analysis detected 35 up- and 80 down-regulated lncRNAs in HCC samples compared with adjacent normal samples. In addition, five differentially expressed lncRNAs were predicted to play a role in oxidation and reduction process. With regard to splicing alterations, we identified nine highly recurrent differential splicing events belonging to eight genes USO1, RPS24, CCDC50, THNSL2, NUMB, FN1 (two events), SLC39A14 and NR1I3. Of them, splicing alterations of SLC39A14 and NR1I3 were reported for the association with HCC for the first time. The splicing dysregulation in HCC may be influenced by three splicing factors ESRP2, CELF2 and SRSF5 which were significantly down-regulated in HCC samples. This study revealed uncharacterized aspects of HCC transcriptome and identified important lncRNAs and splicing isoforms with the potential to serve as biomarkers and therapeutic targets for the disease.

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Section: Discussionsupporting

confidence: 80%

Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets

Zhang

Liu²,

Zhang

et al. 2015

Mol Genet Genomics

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“…Analysis of ucRNA targets in PCa has identified more than 1,000 possible ucRNA-mRNA interactions, with enrichment of ucRNA targets in pathways related to calcium binding and RAS signaling. 30 Recent advances in transcriptomic sequencing have led to the discovery of many new lncRNAs associated with prostate malignancies 31,32 and have allowed re-evaluation of other known cancer-associated lncRNAs whose functions have remained unknown for decades ( Table 2). Taken together, these findings highlight the importance of lncRNAs in cancer processes and provide a better understanding of the impact that lncRNAs will have in comprehending the regulation of gene expression in cancer, especially in relation to the diagnosis and treatment of cancer.…”

Section: Long Noncoding Rnas In Prostate Cancermentioning

confidence: 99%

“…Emerging data are beginning to link diverse mutations in lncRNA genes with distinct types of cancer. 32,71 However, the precise mechanism by which lncRNA variants contribute to carcinogenesis remains a mystery.…”

Section: Future Perspectivesmentioning

confidence: 99%

Long noncoding RNAs in prostate cancer: mechanisms and applications

Yang

Lin

2014

Molecular & Cellular Oncology

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A large proportion of the control of gene expression in humans is mediated by noncoding elements in the genome. Long noncoding RNAs (lncRNAs) have emerged as a new class of pivotal regulatory components, orchestrating extensive cellular processes and connections. LncRNAs play various roles from chromatin modification to alternative splicing and post-transcriptional processing and are involved in almost all aspects of eukaryotic regulation. LncRNA-based mechanisms modulate cell fates during development, and their dysregulation underscores many human disorders, especially cancer, through chromosomal translocation, deletion, and nucleotide expansions. Recent studies demonstrate that multiple prostate cancer risk loci are associated with lncRNAs and that ectopic expression of these transcripts triggers a cascade of cellular events driving tumor initiation and progression. The recent increased rate of discovery of lncRNAs has been leveraged for application in clinical strategies such as novel biomarkers and therapeutic targets. Despite this potential, many issues remain to be addressed in this fast-growing field.

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“…Esteve-Codina et al also used RNA-seq to identify a set of 2047 putative lncRNAs from two phenotypically different pigs [103]. More recently, RNA-seq analysis has been used to identify cancer-associated lncRNAs in prostate cancer [104], long intergenic transcripts involved in adipogenesis [105], and differentially expressed lncRNAs in pancreatic islet cells [106]. In a study of 10 cancer cell lines, Chen et al used RNA-seq to identify differentially expressed lncRNAs that were correlated with certain cancer types [107].…”

Section: Transcriptome Analysismentioning

confidence: 99%

Long Noncoding RNAs and Cancer

Wright

2015

Epigenetic Cancer Therapy

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RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings

Cited by 43 publications

References 0 publications

Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets

Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets

Long noncoding RNAs in prostate cancer: mechanisms and applications

Long Noncoding RNAs and Cancer

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