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Transcriptome‐Wide Analysis Reveals the Landscape of Aberrant Alternative Splicing Events in Liver Cancer
Author(s) -
Li Shengli,
Hu Zhixiang,
Zhao Yingjun,
Huang Shenglin,
He Xianghuo
Publication year - 2019
Publication title -
hepatology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.488
H-Index - 361
eISSN - 1527-3350
pISSN - 0270-9139
DOI - 10.1002/hep.30158
Subject(s) - biology , alternative splicing , gene , transcriptome , rna splicing , genetics , computational biology , gene isoform , rna , transcription factor , gene expression
Alternative splicing (AS) is assumed to be a pivotal determinant for the generation of diverse transcriptional variants in cancer. However, the comprehensive dysregulation of AS and the prospective biological and clinical relevance in hepatocellular carcinoma (HCC) remain obscure. Here, we identified and depicted the AS landscape in HCC by performing reference‐based assembly of sequencing reads from over 600 RNA sequencing (RNA‐seq) libraries. We detected various differentially spliced ASEs across patients covering not only protein‐coding genes, but also considerable numbers of noncoding genes. Strikingly, alternative transcription initiation was found to frequently occur in HCC. These differential ASEs were highly related to “cancer hallmarks” and involved in metabolism‐related pathways in particular. In addition, 243 differential ASEs were identified as risk predictors for HCC patient survival. The isoform switch of metabolism‐related gene UGP2 (UDP‐glucose pyrophosphorylase 2) might play an essential role in HCC. We further constructed regulatory networks between RNA‐binding protein (RBP) genes and the corresponding ASEs. Further analysis demonstrated that the regulated networks were enriched in a variety of metabolism‐related pathways. Conclusion: Differential ASEs are prevalent in HCC, where alternative transcription initiation was found to frequently occur. We found that genes having differential ASEs were significantly enriched in metabolism‐related pathways. The expression variations, binding relations, and even mutations of RBP genes largely influenced differential ASEs in HCC.