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Functional divergence and convergence between the transcript network and gene network in lung adenocarcinoma

Authors Hsu M, Pan C, Chen F

Received 21 August 2015

Accepted for publication 10 December 2015

Published 14 January 2016 Volume 2016:9 Pages 335—347


Checked for plagiarism Yes

Review by Single-blind

Peer reviewer comments 4

Editor who approved publication: Dr Faris Farassati

Min-Kung Hsu,1 Chia-Lin Pan,2 Feng-Chi Chen1–3

1Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu, 2Institute of Population Health Sciences, National Health Research Institutes, Zhunan, 3School of Dentistry, China Medical University, Taichung, Taiwan

Introduction: Alternative RNA splicing is a critical regulatory mechanism during tumorigenesis. However, previous oncological studies mainly focused on the splicing of individual genes. Whether and how transcript isoforms are coordinated to affect cellular functions remain underexplored. Also of great interest is how the splicing regulome cooperates with the transcription regulome to facilitate tumorigenesis. The answers to these questions are of fundamental importance to cancer biology.
Results: Here, we report a comparative study between the transcript-based network (TN) and the gene-based network (GN) derived from the transcriptomes of paired tumor–normal tissues from 77 lung adenocarcinoma patients. We demonstrate that the two networks differ significantly from each other in terms of patient clustering and the number and functions of network modules. Interestingly, the majority (89.5%) of multi-transcript genes have their transcript isoforms distributed in at least two TN modules, suggesting regulatory and functional divergences between transcript isoforms. Furthermore, TN and GN modules share only ~50%–60% of their biological functions. TN thus appears to constitute a regulatory layer separate from GN. Nevertheless, our results indicate that functional convergence and divergence both occur between TN and GN, implying complex interactions between the two regulatory layers. Finally, we report that the expression profiles of module members in both TN and GN shift dramatically yet concordantly during tumorigenesis. The mechanisms underlying this coordinated shifting remain unclear yet are worth further explorations.
Conclusion: We show that in lung adenocarcinoma, transcript isoforms per se are coordinately regulated to conduct biological functions not conveyed by the network of genes. However, the two networks may interact closely with each other by sharing the same or related biological functions. Unraveling the effects and mechanisms of such interactions will significantly advance our understanding of this deadly disease.

Keywords: lung adenocarcinoma, transcriptome analysis, gene network, module, alternative splicing, transcriptional regulation

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