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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Oncol. | doi: 10.3389/fonc.2018.00537

Genome-wide profiling of prognostic alternative splicing signature in colorectal cancer

Zhen Zong1, Hui Li2, Chenghao Yi1, Houqun Ying1, Zhengming Zhu1* and  Wang He1*
  • 1Second Affiliated Hospital of Nanchang University, China
  • 2First Affiliated Hospital of Nanchang University, China

Background: A systematic examination of prognostic alternative splicing(AS) events in patients with colorectal cancer(CRC) was not well illustrated. This study was to explore differential RNA splicing patterns and elucidate the function of the splice variants served as prognostic biomarkers in colorectal cancer(CRC).
Methods: Genome-wide profiling of prognostic alternative splicing(AS) events using RNA-seq data from The Cancer Genome Atlas(TCGA) program was conducted to evaluate the roles of seven AS patterns in 330 colorectal cancer cohort. The prognostic predictors models were assessed by integrated Cox proportional hazards regression. Based on the correlations between survival associated AS events and splicing factors, splicing networks were built.
Results: A total of 2158 survival associated AS events in CRC were identified. Interestingly, most of these top twenty survival associated AS events were adverse prognostic factors. The prognostic models were built by each type of splicing patterns, performing well for risk stratification in CRC patients. The area under curve(AUC) of receiver operating characteristic(ROC) for the combined prognostic predictors model could reach 0.963. Splicing network also suggested distinguished correlation between the expression of splicing factors and AS events in CRC patients.
Conclusion: The ideal prognostic predictors model for risk stratification in CRC patients was constructed by differential splicing patterns of thirteen genes. Our findings enriched knowledge about differential RNA splicing patterns and the regulation of splicing, providing generous biomarker candidates and potential targets for the treatment of CRC.

Keywords: Alternative Splicing, colorectal cancer, Survival, splicing factor, prognosis

Received: 13 Aug 2018; Accepted: 31 Oct 2018.

Edited by:

Michael J. Wargovich, The University of Texas Health Science Center at San Antonio, United States

Reviewed by:

Cornelis F. Sier, Leiden University, Netherlands
Frederique VEGRAN, INSERM U1231 Lipides, Nutrition, Cancer (LNC), France  

Copyright: © 2018 Zong, Li, Yi, Ying, Zhu and He. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Prof. Zhengming Zhu, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China, 371413659@qq.com
Dr. Wang He, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China, wanghe0936@163.com