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J Genet Genomics. 2015 Oct 20;42(10):579-587. doi: 10.1016/j.jgg.2015.09.007. Epub 2015 Sep 30.

Integrative Analyses of Lung Squamous Cell Carcinoma in Ten Chinese Patients with Transcriptome Sequencing.

Author information

1
Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
2
Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China; The First Clinic College of South China University of Technology, Guangzhou 510080, China.
3
Burning Rock Biotech, Guangzhou 510300, China.
4
First Department of Chemotherapy, Meizhou People Hospital, Meizhou, Guangdong 514000, China.
5
Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China; The First Clinic College of South China University of Technology, Guangzhou 510080, China. Electronic address: syylwu@live.cn.

Abstract

Few effective therapies have been developed for the treatment of lung squamous cell carcinoma (SQCC), in part due to a lack of understanding regarding the mechanisms underlying the initiation and development of this disease. Whole transcriptome sequencing not only provides insight into the expression of all transcribed genes, but offers an efficient approach for identifying genetic variations, including gene fusions, mutations and alternative splicing. In this study, we performed whole transcriptome sequencing of 10 patients with stage IIIA lung SQCC, and discovered a large number of single nucleotide variants (SNVs; mean of 12.2 SNVs/Mb), with C>T/G>A and A>G/T>C transitions being the most frequently observed. Additionally, a total of 132 gene fusions were identified based upon TopHat alignments, 70.5% (93/132) of which occurred as a result of intra-chromosomal rearrangements. Based on the number of supporting reads for each fusion, we further validated 20 of the 26 top gene fusions by RT-PCR and Sanger sequencing. Taken together, these data provide an in-depth view of transcriptional alterations in lung SQCC patients, and may be useful for identification of new therapeutic targets.

KEYWORDS:

Gene fusion; Lung squamous cell carcinoma; Transcriptome sequencing

PMID:
26554911
DOI:
10.1016/j.jgg.2015.09.007
[Indexed for MEDLINE]

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