Dataset Information

Comprehensive analysis of microRNAs in breast cancer.

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.

SUBMITTER: Chang HT

PROVIDER: S-EPMC3521236 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Comprehensive analysis of microRNAs in breast cancer.

Chang Hong-Tai HT Li Sung-Chou SC Ho Meng-Ru MR Pan Hung-Wei HW Ger Luo-Ping LP Hu Ling-Yueh LY Yu Shou-Yu SY Li Wen-Hsiung WH Tsai Kuo-Wang KW

BMC genomics 20121213

<h4>Background</h4>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 sh ...[more]

PMID: 23281739

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Project description:Colorectal cancer (CRC) has been defined as a common malignancy due to its prevailing incidence in both males and females. Recently, the intrinsic value of microRNAs (miRNAs) with respect to early cancer diagnosis has been contentious as the diagnostic accuracy of miRNAs significantly varied across different studies. As a result of this, this pioneer meta-analysis was proposed to address this issue. Qualified studies were obtained through electronic systematical searching in Medline, Embase, and PubMed. On the basis of the random-effects model, we calculated the pooled sensitivity (SEN), specificity (SPE), and area under the receiver operating characteristics curve (AUC) to assess the diagnostic accuracy of miRNAs. Subgroup analysis and meta-regression were implemented to determine how different confounding factors affect the overall diagnostic accuracy which were considered important sources of heterogeneity. All the statistical analyses were conducted with R 3.2.1 software. We incorporated 103 studies from 36 articles with a total of 3124 CRC patients and 2579 healthy individuals. MiRNAs have a good performance with the following pooled estimates: SEN = 0.769 (95% CI = 0.733-0.802), SPE = 0.806 (95% CI = 0.781-0.829), AUC = 0.857, and partial AUC = 0.773. As suggested by subgroup analyses and meta-regression, multiple miRNAs appeared to be more favorable than single miRNA (AUC: 0.918 > 0.813, partial AUC: 0.848 > 0.701, sensitivity = 0.853 > 0.718, specificity = 0.860 > 0.772). Compared with samples of plasma, blood, tissue, and feces, miRNA obtained from serum samples were more powerful for detecting CRC particularly in Asian. Our study provided exclusive evidence that multiple miRNAs extracted from serum samples had superior diagnostic performance over single miRNA for screening CRC. Therefore, this approach that is characterized by high specificity and noninvasive nature may assist in early diagnosis of CRC particularly in Asian.

Dataset Information

Comprehensive analysis of microRNAs in breast cancer.

Publications

Comprehensive analysis of microRNAs in breast cancer.

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