Comprehensive analysis of microRNAs in breast cancer

Hong-Tai Chang,Wen-Hsiung Li,Kuo-Wang Tsai,Ling-Yueh Hu,Luo-Ping Ger,Hung-Wei Pan,Shou-Yu Yu,Meng-Ru Ho,Sung-Chou Li

doi:10.1186/1471-2164-13-s7-s18

Abstract

BackgroundMicroRNAs (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.MethodsNext-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.ResultsThe 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.ConclusionsExpression 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.

Highlights

MicroRNAs are short noncoding RNAs that play important roles in breast cancer progression by downregulating gene expression
Analysis of miRNA sequence reads After subjecting the downloaded small RNA reads to the 3’ adaptor trimming procedure, the normal library contained approximately 2.7 million clean reads and the tumor library approximately 38.3 million clean reads (Table 1)
The libraries contained an unequal number of initially used reads; comparisons in miRNA expression between the libraries were performed using the unit of transcript per million (TPM)

Summary

Introduction

MicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in breast cancer progression by downregulating gene expression. 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. The pri-miRNAs are processed by Drosha, forming the precursor miRNAs (pre-miRNAs), composed of a 5p arm, a 3p arm, and a terminal loop, approximately 70 nucleotides in length. Following the transport of pre-miRNAs to the cytoplasm by exportin 5, they are further processed by Dicer to release the terminal loop and the duplex (5p arm/ 3p arm), 22 nucleotides in length. Fernandez-Valverde et al [6] reported that miR-282 and miR-312a are enriched for 3’ adenosine additions during early embryonic development, which increases miRNA stability or enhances miRNA and mRNA interaction

Methods

Results

Conclusion