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Open Access Research article

The global landscape of intron retentions in lung adenocarcinoma

Qu Zhang1*, Hua Li2, Hong Jin2, Huibiao Tan2, Jun Zhang3 and Sitong Sheng245*

Author Affiliations

1 Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA

2 HYK High-throughput Biotechnology Institute, 4/F, Building #11, Software Park, 2nd Central Keji Rd, Hi-Tech Industrial Park, Shenzhen 518060, China

3 Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No.197 Ruijin 2nd Road, Shanghai 200025, China

4 School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China

5 College of Life Sciences, Shenzhen University, Shenzhen 518060, China

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BMC Medical Genomics 2014, 7:15  doi:10.1186/1755-8794-7-15

Published: 20 March 2014



The transcriptome complexity in an organism can be achieved by alternative splicing of precursor messenger RNAs. It has been revealed that alternations in mRNA splicing play an important role in a number of diseases including human cancers.


In this study, we exploited whole transcriptome sequencing data from five lung adenocarcinoma tissues and their matched normal tissues to interrogate intron retention, a less studied alternative splicing form which has profound structural and functional consequence by modifying open reading frame or inserting premature stop codons.


Abundant intron retention events were found in both tumor and normal tissues, and 2,340 and 1,422 genes only contain tumor-specific retentions and normal-specific retentions, respectively. Combined with gene expression analysis, we showed that genes with tumor-specific retentions tend to be over-expressed in tumors, and the abundance of intron retention within genes is negatively related with gene expression, indicating the action of nonsense mediated decay. Further functional analysis demonstrated that genes with tumor-specific retentions include known lung cancer driver genes and are found enriched in pathways important in carcinogenesis.


We hypothesize that intron retentions and consequent nonsense mediated decay may collectively counteract the over-expression of genes promoting cancer development. Identification of genes with tumor-specific retentions may also help develop targeted therapies.

Intron retentions; RNA-Seq; Lung adenocarcinoma; Gene expression; Nonsense mediated decay