+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification

Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification

Plos One 8(11): E80306

Long non-coding RNAs (lncRNAs) are emerging as potent regulators of cell physiology, and recent studies highlight their role in tumor development. However, while established protein-coding oncogenes and tumor suppressors often display striking patterns of focal DNA copy-number alteration in tumors, similar evidence is largely lacking for lncRNAs. Here, we report on a genomic analysis of GENCODE lncRNAs in high-grade serous ovarian adenocarcinoma, based on The Cancer Genome Atlas (TCGA) molecular profiles. Using genomic copy-number data and deep coverage transcriptome sequencing, we derived dual copy-number and expression data for 10,419 lncRNAs across 407 primary tumors. We describe global correlations between lncRNA copy-number and expression, and associate established expression subtypes with distinct lncRNA signatures. By examining regions of focal copy-number change that lack protein-coding targets, we identified an intergenic lncRNA on chromosome 1, OVAL, that shows narrow focal genomic amplification in a subset of tumors. While weakly expressed in most tumors, focal amplification coincided with strong OVAL transcriptional activation. Screening of 16 other cancer types revealed similar patterns in serous endometrial carcinomas. This shows that intergenic lncRNAs can be specifically targeted by somatic copy-number amplification, suggestive of functional involvement in tumor initiation or progression. Our analysis provides testable hypotheses and paves the way for further study of lncRNAs based on TCGA and other large-scale cancer genomics datasets.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 052269819

Download citation: RISBibTeXText

PMID: 24265805

DOI: 10.1371/journal.pone.0080306

Related references

Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes. Oncotarget 5(20): 9864-9876, 2015

RNA-Seq analysis of non-small cell lung cancer in female never-smokers reveals candidate cancer-associated long non-coding RNAs. Pathology, Research and Practice 212(6): 549-554, 2017

Long non-coding RNAs expression profile in HepG2 cells reveals the potential role of long non-coding RNAs in the cholesterol metabolism. Chinese Medical Journal 128(1): 91-97, 2015

Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types. Oncotarget 7(23): 35044-35055, 2018

Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs. Bmc Genomics 17(1): 841, 2016

Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development 140(13): 2828-2834, 2013

Integrated analysis of long non-coding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in gastric cancer pathogenesis. International Journal of Oncology 45(2): 619-628, 2015

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination. Plos Genetics 11(12): E1005669, 2016

Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL. Clinical Epigenetics 8: 106, 2016

Consensus Analysis of Whole Transcriptome Profiles from Two Breast Cancer Patient Cohorts Reveals Long Non-Coding RNAs Associated with Intrinsic Subtype and the Tumour Microenvironment. Plos One 11(9): E0163238, 2018

Long non-coding RNAs in ovarian cancer. Journal of Experimental and Clinical Cancer Research 37(1): 120, 2018

Protein-coding genes, long non-coding RNAs combined with microRNAs as a novel clinical multi-dimension transcriptome signature to predict prognosis in ovarian cancer. Oncotarget 8(42): 72847-72859, 2017

The Role of Long Non-Coding RNAs in Ovarian Cancer. Iranian Biomedical Journal 21(1): 3-15, 2016

Comprehensive analysis of key genes, microRNAs and long non-coding RNAs in hepatocellular carcinoma. Febs Open Bio 8(9): 1424-1436, 2018

Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs. Genome Biology 17: 19, 2016