1. Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method
- Author
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Zhenbo Hou, Haiyan Cui, Mingyue Li, Dengguo Chen, Yu Ding, Xinmei Wang, Hongmei Han, Baohua Zhang, Hengming Zhang, Liang Li, Yuqian Tao, Yingchun Yin, Xinyun Wang, and Jianzhao Li
- Subjects
Untranslated region ,Adult ,Candidate gene ,Polyadenylation ,education ,Breast Neoplasms ,subtypes in breast cancer ,Breast cancer ,breast cancer ,Genetics ,Biomarkers, Tumor ,Medicine ,Humans ,RNA, Messenger ,RNA Processing, Post-Transcriptional ,tandem 3′ untranslated region ,Gene ,3' Untranslated Regions ,Neoplasm Staging ,Messenger RNA ,business.industry ,profile of alternative adenylation sites ,Computational Biology ,Reproducibility of Results ,Molecular Sequence Annotation ,General Medicine ,Sequence Analysis, DNA ,Articles ,Cell cycle ,Middle Aged ,medicine.disease ,Molecular medicine ,sequencing alternative polyadenylation sites ,Cancer research ,Female ,business - Abstract
Breast cancer (BC) is a leading cause of cancer-related mortality in females and is recognized as a molecularly heterogeneous disease. Previous studies have suggested that alternative messenger RNA (mRNA) processing, particularly alternative polyadenylation [poly(A)] (APA), can be a powerful molecular biomarker with prognostic potential. Therefore, in the present study, we profiled APA sites in the luminal B subtype of BC by sequencing APA sites (SAPAS) method, in order to assess the relation of these APA site-switching events to the recognized molecular subtypes of BC, and to discover novel candidate genes and pathways in BC. Through comprehensive analysis, the trend of APA site-switching events in the 3′ untranslated regions (3′UTRs) in the luminal B subtype of BC were found to be the same as that in MCF7 cell lines. Among the genes involved in the events, a significantly greater number of genes was found with shortened 3′UTRs in the samples, which were samples of primary cancer with relatively low proliferation. These findings may provide novel information for the clinical diagnosis and prognosis on a molecular level. Several potential biomarkers with significantly differential tandem 3′UTRs and expression were found and validated. The related biological progresses and pathways involved were partly confirmed by other studies. In conclusion, this study provides new insight into the diagnosis and prognosis of BC from the APA site profile aspect.
- Published
- 2014