Tuberc Respir Dis.  2016 Apr;79(2):85-90. 10.4046/trd.2016.79.2.85.

Identification of Alternative Splicing and Fusion Transcripts in Non-Small Cell Lung Cancer by RNA Sequencing

• Hong Y
• Kim WJ
• Bang CY
• Lee JC
• Oh YM

• KMID: 2320770
• DOI: http://doi.org/10.4046/trd.2016.79.2.85

Abstract

BACKGROUND
Lung cancer is the most common cause of cancer related death. Alterations in gene sequence, structure, and expression have an important role in the pathogenesis of lung cancer. Fusion genes and alternative splicing of cancer-related genes have the potential to be oncogenic. In the current study, we performed RNA-sequencing (RNA-seq) to investigate potential fusion genes and alternative splicing in non-small cell lung cancer.
METHODS
RNA was isolated from lung tissues obtained from 86 subjects with lung cancer. The RNA samples from lung cancer and normal tissues were processed with RNA-seq using the HiSeq 2000 system. Fusion genes were evaluated using Defuse and ChimeraScan. Candidate fusion transcripts were validated by Sanger sequencing. Alternative splicing was analyzed using multivariate analysis of transcript sequencing and validated using quantitative real time polymerase chain reaction.
RESULTS
RNA-seq data identified oncogenic fusion genes EML4-ALK and SLC34A2-ROS1 in three of 86 normal-cancer paired samples. Nine distinct fusion transcripts were selected using DeFuse and ChimeraScan; of which, four fusion transcripts were validated by Sanger sequencing. In 33 squamous cell carcinoma, 29 tumor specific skipped exon events and six mutually exclusive exon events were identified. ITGB4 and PYCR1 were top genes that showed significant tumor specific splice variants.
CONCLUSION
In conclusion, RNA-seq data identified novel potential fusion transcripts and splice variants. Further evaluation of their functional significance in the pathogenesis of lung cancer is required.

Keyword

Sequence Analysis; RNA; Alternative Splicing; Gene Fusion; Lung Neoplasms

MeSH Terms

Alternative Splicing*
Carcinoma, Non-Small-Cell Lung*
Carcinoma, Squamous Cell
Exons
Gene Fusion
Lung
Lung Neoplasms
Multivariate Analysis
Real-Time Polymerase Chain Reaction
RNA*
Sequence Analysis
Sequence Analysis, RNA*
RNA

Figure

• 

  Figure 1 Confirmation by Sanger sequencing of fusion transcript structure according to presence of exon of genes. (A) PFKFB3-AL137145.2. (B) KLHL2-C4orf3. (C) TPPP-BRD9. (D) HNRNPA2B1-SKAP2. The black arrows indicate orientations.

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