Search Results for: long noncoding rna expression

Genome-wide analysis of long noncoding RNA signature in human colorectal cancer

Long noncoding RNAs (lncRNAs) have been widely regarded as crucial regulators in various biological processes involved in carcinogenesis. However, the comprehensive lncRNA expression signature in colorectal cancer remains fully unknown. Researchers at Nanjing Medical University performed a high throughput microarray assay to detect lncRNA expression profile in three paired human colorectal cancer tissues and their adjacent normal tissues. Additional 90 paired colorectal samples were collected to verify differently expression levels of two selected lncRNAs using q-RT-PCR assay. Bioinformatic approaches were performed to explore into the functions of these differently expressed lncRNAs.

Microarray assay showed a series of lncRNAs were differently expressed in colorectal cancer. Two of the lncRNAs, HOTAIR and a novel lncRNA, lncRNA-422 were confirmed in more samples (P=0.015 for HOTAIR and P=0.027 for lncRNA-422, respectively). GSEA indicated that gene sets most correlated with them were those named up-regulated in KRAS-over, down-regulated in JAK2-knockout, down-regulated in PDGF-over and down-regulated in TBK1-knockout, all of which were cancer-related. Subsequently, GO analyses of most significantly correlated coding genes of HOTAIR and lncRNA-422 showed that these two lncRNAs may participate in carcinogenesis by regulating protein coding genes involved in special biological process relevant to cancer.

This study demonstrated that different lncRNA expression patterns were involved in colorectal cancer. Besides, HOTAIR and lncRNA-422 were identified to participate in colorectal cancer. Further studies into biological mechanisms of differently expressed lncRNAs identified in this study will help to provide new perspective in colorectal cancer pathogenesis.

lncRNA

  • Xue Y, Ma G, Gu D, Zhu L, Hua Q, Du M, Chu H, Tong N, Chen J, Zhang Z, Wang M. (2014) Genome-wide analysis of long noncoding RNA signature in human colorectal cancer. Gene [Epub ahead of print]. [abstract]

Incoming search terms:

  • seqlnc

LncRNA2Target – a database for differentially expressed genes after lncRNA knockdown or overexpression

Long noncoding RNAs (lncRNAs) have been emerged as critical regulators of gene expression at epigenetic, transcriptional and post-transcriptional level, yet what genes are regulated by lncRNAs remains to be characterized. To assess the effects of a specific lncRNA on gene expression, increasing researchers profiled the genome-wide or individual gene expression level changes after knocking down or overexpressing the lncRNA. However, no online repository is currently available to collect these differentially expressed genes regulated by lncRNAs.

To make it convenient for researchers to know what genes are regulated by a lncRNA or which lncRNAs regulate a given gene of interest, researchers at the Harbin Institute of Technology have developed LncRNA2Target: a comprehensive resource of differentially expressed genes after lncRNA knockdown or overexpression.

lncRNA

In this database system, target genes of a lncRNA are defined as the differentially expressed genes after knocking down or overexpressing the lncRNA. By reviewing all published lncRNA papers, we manually curated the differentially expressed target genes confirmed by qRT-PCR or western blot, and identified all the differential target genes from the microarray or RNA-seq data.

Availability – the LncRNA2Target database is available at: http://www.lncrna2target.org/

The long non-coding RNA NBAT-1 is a prognostic biomarker in neuroblastoma

lncRNA

Neuroblastoma is an embryonal tumor of the sympathetic nervous system and the most common extracranial tumor of childhood. By sequencing transcriptomes of low- and high-risk neuroblastomas, we detected differentially expressed annotated and nonannotated long noncoding RNAs (lncRNAs). We identified a lncRNA neuroblastoma associated transcript-1 (NBAT-1) as a biomarker significantly predicting clinical outcome of neuroblastoma. CpG methylation and a high-risk neuroblastoma associated SNP on chromosome 6p22 functionally contribute to NBAT-1 differential expression. Loss of NBAT-1 increases cellular proliferation and invasion. It controls these processes via epigenetic silencing of target genes. NBAT-1 loss affects neuronal differentiation through activation of the neuronal-specific transcription factor NRSF/REST. Thus, loss of NBAT-1 contributes to aggressive neuroblastoma by increasing proliferation and impairing differentiation of neuronal precursors.

  • Gaurav Kumar Pandey, Sanhita Mitra, Santhilal Subhash, Falk Hertwig, Meena Kanduri, Kankadeb Mishra, Susanne Fransson, Abiarchana Ganeshram, Tanmoy Mondal, Sashidhar Bandaru, Malin Östensson, Levent M. Akyürek, Jonas Abrahamsson, Susan Pfeifer, Erik Larsson, Leming Shi, Zhiyu Peng, Matthias Fischer, Tommy Martinsson, Fredrik Hedborg, Per Kogner, Chandrasekhar Kanduri. (2014) The Risk-Associated Long Noncoding RNA NBAT-1 Controls Neuroblastoma Progression by Regulating Cell Proliferation and Neuronal Differentiation. Cancer Cell 26(5): 722–737. [abstract]

Expanding the functional role of long noncoding RNA

New findings bring to light a previously unappreciated mechanism involved in the regulation of the oncoprotein MYC. Interesting observations find that the long noncoding RNA (lncRNA) PVT1 is active in controlling levels of MYC through regulation of MYC protein stability.

lncRNA

In normal cells, MYC is targeted by phosphorylation on threonine 58 (Thr58) and becomes destabilized and degraded. (B) In cancer cells, gain of 8q24 promotes the expression of MYC and PVT1. PVT1 interferes with the phosphorylation of Thr58 on MYC, which stabilizes the protein and increases its level.

  • Johnsson P, Morris KV. (2014) Expanding the functional role of long noncoding RNAs. Cell Res [Epub ahead of print]. [article]

LncRNA: A link between RNA and cancer

Unraveling the gene expression networks governing cancer initiation and development is essential while remains largely uncompleted. With the innovations in RNA-seq technologies and computational biology, long noncoding RNAs (lncRNAs) are being identified and characterized at a rapid pace. Recent findings reveal that lncRNAs are implicated in serial steps of cancer development. These lncRNAs interact with DNA, RNA, protein molecules and/or their combinations, acting as an essential regulator in chromatin organization, transcriptional and post-transcriptional regulation. Their misexpression confers the cancer cell capacities for tumor initiation, growth, and metastasis. The review here will emphasize their aberrant expression and function in cancer, and the roles in cancer diagnosis and therapy will be also discussed.

lncRNA

  • Yanga G, Lub X, Yuanc L. (2014) LncRNA: A link between RNA and cancer. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms [Epub ahead of print]. [abstract]