title: Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method.
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.
authors.affiliation: Department of Pathology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Xinmei
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Neurology, The First Affiliated Hospital of Zhongshan University, Guangzhou, Guangdong 510080, P.R. China.
authors.forename: Mingyue
authors.initials: M
authors.lastname: Li
authors.affiliation: Department of Pathology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Yingchun
authors.initials: Y
authors.lastname: Yin
authors.affiliation: Department of Breast and Thyroid Surgery, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Liang
authors.initials: L
authors.lastname: Li
authors.affiliation: Department of Neurology, The First Affiliated Hospital of Zhongshan University, Guangzhou, Guangdong 510080, P.R. China.
authors.forename: Yuqian
authors.initials: Y
authors.lastname: Tao
authors.affiliation: Department of Neurology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Dengguo
authors.initials: D
authors.lastname: Chen
authors.affiliation: Department of Pathology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Jianzhao
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Pathology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Hongmei
authors.initials: H
authors.lastname: Han
authors.affiliation: Department of Pathology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Zhenbo
authors.initials: Z
authors.lastname: Hou
authors.affiliation: Department of Pathology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Baohua
authors.initials: B
authors.lastname: Zhang
authors.affiliation: Department of Pathology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Xinyun
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Neurology, The First Affiliated Hospital of Zhongshan University, Guangzhou, Guangdong 510080, P.R. China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Ding
authors.affiliation: Department of Pathology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Cui
authors.affiliation: Department of Pathology, The Central Hospital of Zibo, Zibo, Shandong 255036, P.R. China.
authors.forename: Hengming
authors.initials: H
authors.lastname: Zhang
mesh_terms: D020413:3' Untranslated Regions; D000328:Adult; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology*; D019295:Computational Biology; D005260:Female; D006801:Humans; D008875:Middle Aged; D058977:Molecular Sequence Annotation; D009367:Neoplasm Staging; D026723:Polyadenylation; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D020413:3' Untranslated Regions; D014408:Biomarkers, Tumor; D012333:RNA, Messenger