A pan-cancer study of copy number gain and up-regulation in human oncogenes

Yong Kiat Wee; Tianfang Wang; Yining Liu; Xiaoyan Li; Min Zhao

doi:10.1016/j.lfs.2018.09.032

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A pan-cancer study of copy number gain and up-regulation in human oncogenes

Journal article

Peer reviewed

A pan-cancer study of copy number gain and up-regulation in human oncogenes

Yong Kiat Wee, Tianfang Wang, Yining Liu, Xiaoyan Li and Min Zhao

Life Sciences, Vol.211, pp.206-214

2018

DOI: https://doi.org/10.1016/j.lfs.2018.09.032

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Abstract

oncogene

pan-cancer

copy number variation

copy number gain

gene expression

Aim: There has been limited research on CNVs in oncogenes and we conducted a systematic pan-cancer analysis of CNVs and their gene expression changes. The aim of the present study was to provide an insight into the relationships between gene expression and oncogenesis. Main methods: We collected all the oncogenes from ONGene database and overlapped with CNVs TCGA tumour samples from Catalogue of Somatic Mutations in Cancer database. We further conducted an integrative analysis of CNV with gene expression using the data from the matched TCGA tumour samples. Key findings: From our analysis, we found 637 oncogenes associated with CNVs in 5900 tumour samples. There were 204 oncogenes with frequent copy number of gain (CNG). These 204 oncogenes were enriched in cancer-related pathways including the MAPK cascade and Ras GTPases signalling pathways. By using corresponding tumour samples data to perform integrative analyses of CNVs and gene expression changes, we identified 95 oncogenes with consistent CNG occurrence and up-regulation in the tumour samples, which may represent the recurrent driving force for oncogenesis. Surprisingly, eight oncogenes shown concordant CNG and gene up-regulation in at least 250 tumour samples: INTS8 (355), ECT2 (326), LSM1 (310), DDHD2 (298), COPS5 (286), EIF3E (281), TPD52 (258) and ERBB2 (254). Significance: As the first report about abundant CNGs on oncogene and concordant change of gene expression, our results may be valuable for the design of CNV-based cancer diagnostic strategy.

Details

Title: A pan-cancer study of copy number gain and up-regulation in human oncogenes
Authors: Yong Kiat Wee (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Tianfang Wang (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Yining Liu (Author) - Guangzhou Medical University, China
Xiaoyan Li (Author) - Capital Medical University, China
Min Zhao (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Publication details: Life Sciences, Vol.211, pp.206-214
Publisher: Elsevier Inc.
DOI: 10.1016/j.lfs.2018.09.032
ISSN: 0024-3205
Organisation Unit: Centre for Bioinnovation; School of Science, Technology and Engineering; University of the Sunshine Coast, Queensland; School of Science and Engineering - Legacy; GeneCology Research Centre - Legacy
Language: English
Record Identifier: 99451254002621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Medicine, Research & Experimental; Pharmacology & Pharmacy

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