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This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology

Open Access Proceedings

Comprehensive analysis of microRNAs in breast cancer

Hong-Tai Chang12, Sung-Chou Li3, Meng-Ru Ho4, Hung-Wei Pan5, Luo-Ping Ger5, Ling-Yueh Hu6, Shou-Yu Yu5, Wen-Hsiung Li47 and Kuo-Wang Tsai58*

Author Affiliations

1 Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, Republic of China

2 Department of Emergency, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, Republic of China

3 Genomics Research Center, Academia Sinica, Taipei, Taiwan, Republic of China

4 Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China

5 Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, Republic of China

6 Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, Republic of China

7 Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA

8 Department of Biotechnology, Tajen University, Taiwan, Republic of China

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BMC Genomics 2012, 13(Suppl 7):S18  doi:10.1186/1471-2164-13-S7-S18

Published: 13 December 2012

Abstract

Background

MicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in breast cancer progression by downregulating gene expression. The detailed mechanisms and biological functions of miRNA molecules in breast carcinogenesis have yet to be fully elucidated. This study used bioinformatics and experimental approaches to conduct detailed analysis of the dysregulated miRNAs, arm selection preferences, 3' end modifications, and position shifts in isoforms of miRNAs (isomiRs) in breast cancer.

Methods

Next-generation sequencing (NGS) data on breast cancer was obtained from the NCBI Sequence Read Archive (SRA). The miRNA expression profiles and isomiRs in normal breast and breast tumor tissues were determined by mapping the clean reads back to human miRNAs. Differences in miRNA expression and pre-miRNA 5p/3p arm usage between normal and breast tumor tissues were further investigated using stem-loop reverse transcription and real-time polymerase chain reaction.

Results

The analysis identified and confirmed the aberrant expression of 22 miRNAs in breast cancer. Results from pathway enrichment analysis further indicated that the aberrantly expressed miRNAs play important roles in breast carcinogenesis by regulating the mitogen-activated protein kinase (MAPK) signaling pathway. Data also indicated that the position shifts in isomiRs and 3' end modifications were consistent in breast tumor and adjacent normal tissues, and that 5p/3p arm usage of some miRNAs displayed significant preferences in breast cancer.

Conclusions

Expression pattern and arm selection of miRNAs are significantly varied in breast cancers through analyzing NGS data and experimental approach. These miRNA candidates have high potential to play critical roles in the progression of breast cancer and could potentially provide as targets for future therapy.