Dataset Information

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.

SUBMITTER: Wang X

PROVIDER: S-EPMC4249744 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method.

Wang Xinmei X Li Mingyue M Yin Yingchun Y Li Liang L Tao Yuqian Y Chen Dengguo D Li Jianzhao J Han Hongmei H Hou Zhenbo Z Zhang Baohua B Wang Xinyun X Ding Yu Y Cui Haiyan H Zhang Hengming H

International journal of molecular medicine 20141020 1

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 ...[more]

PMID: 25333330

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Project description:Breast cancer is a common disease with distinct tumor subtypes which can be phenotypically characterized by estrogen receptor, progesterone receptor and HER2/neu receptor status. MiRNAs play regulatory roles in tumor initiation and progression. Altered miRNA expression has been demonstrated in a variety of cancer states to date presenting the potential for exploitation as cancer specific biomarkers. Blood presents an attractive medium biomarker discovery. This study investigated systemic miRNAs differentially expressed in Luminal A (ER+PR+HER2/neu-) breast cancer and their effectiveness as oncologic biomarkers in the clinical setting. Blood samples were prospectively collected from consenting patients with Luminal A breast cancer (n=10) and controls (n=10). RNA was extracted, reverse transcribed and subjected to microarray analysis (n=10 Luminal A; n=10 Control). Differentially expressed miRNAs were identified by artificial neural network (ANN) data-mining algorithms. Ethical approval was granted by the Clinical Research Ethics Committee, Galway Roscommon University Hospital Group. Written informed consent was obtained from all study participants. Blood samples were prospectively collected from 20 women; this included 10 consecutive women with a new diagnosis of Luminal A breast cancer and 10 healthy control participants. Luminal A status was confirmed with immunohistochemistry and fluorescence in situ hybridization (FISH). The blood samples for the healthy control group were collected from women residing in the same catchment area as the cancer cases. These women had no personal history of malignancy and no current inflammatory or infectious condition. Venous non-fasting whole blood samples were collected in BD vacutainers ® containing 18mg dipotassium EDTA anticoagulant (BD-Plymouth, PL6 7BP, UK). Total RNA was extracted from blood (1ml) using TRI Reagent BD (Molecular Research Centre, Inc). RNA concentration and integrity were evaluated by NanoDrop spectrophotometry (NanoDrop ND-1000 Technologies Inc., DE, USA) and Agilent Bioanalyzer RNA 6000 NanoChip Kit Series II (Agilent Technologies, Germany) analysis, respectively. MiRNA microarray profiling Expression profiling of circulating miRNAs was performed using TaqMan miRNA arrays and assays in accordance with the manufacturer’s instructions (Taqman Low Density Array Human microRNA Card A and Card B, Applied Biosystems, Foster City, CA, USA). In short, total RNA was reverse transcribed using Megaplex primer pool A (Applied Biosystems) which contained sequence-specific primers for 381 specific miRNAs plus 3 controls (pool A). An additional panel of 384 miRNAs (381 miRNAs and 3 controls, pool B) was performed on a subset of 4 cancers and 4 controls. Real-time quantitative PCR was performed for 667 miRNAs, using A and B microfluidic cards, each containing primers and probes for 381 specific miRNAs plus 3 controls and thermal-cycled on an Applied Biosystems 7900HT instrument. The TLDA cards contain three endogenous controls (RNU44, RNU48 and MammU6 which is repeated four times on each card). Each card also contains a negative control, an assay unrelated to any human species, ath-miR-159a.

Dataset Information

Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method.

Publications

Profiling of alternative polyadenylation sites in luminal B breast cancer using the SAPAS method.

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