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Genome-wide screen for aberrantly expressed miRNAs reveals miRNA profile signature in breast cancer

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Abstract

Dysregulation in the expression of miRNAs contributes to the occurrence and development of many human cancers. We herein attempted to obtain the potential association between miRNA expression profile and breast cancer by applying high-throughput sequencing technology. Small RNAs from seven paired tumor and adjacent normal tissue samples were sequenced. To determine the miRNA expression profiles in tissues and sera, another five equally pooled serum samples from 20 patients and 30 normal women were sequenced. Despite a similar number in abundantly expressed miRNAs across samples, we detected varying miRNA expression profiles. Some miRNAs showed inconsistent or opposite dysregulation trends across different tumor tissues, including some abundantly expressed miRNA gene clusters and gene families. Wilcoxon sign-rank test for paired samples analysis revealed that abnormal miRNAs showed a higher level of variation across the seven tumor samples. We also completely surveyed abnormal miRNAs expressed in tumor and serum tissues in the mixed datasets based on the relative expression levels. Most of these miRNAs were significantly down-regulated in tumor samples, but nine abnormal miRNAs (miR-18a, 19a, 20a, 30a, 103b, 126, 126*, 192, 1287) were consistently expressed in tumor tissues and serum samples. Based on experimentally validated target mRNAs, functional enrichment analysis indicated that these abnormal miRNAs and miRNA groups (miRNA gene clusters and gene families) have important roles in multiple biological processes. Dynamic miRNA expression profiles, various abnormal miRNA profiles and complexity of the miRNA regulatory network reveal that the miRNA expression profile is a potential biomarker for classifying or detecting human disease.

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Acknowledgments

We appreciate all the patients and healthy controls who participated in this research. We thank Juncheng Dai, Yongyue Wei and Jianling Bai for their help in statistic analysis. The work was supported by National Natural Science Foundation of China (Nos. 30901232, 81072389 and 81102182), China Postdoctoral Science Foundation funded project (No. 2012M521100), University Science Research Project of Jiangsu Province (No. 12KJB310003), Jiangsu Planned Projects for Postdoctoral Research Funds (No. 1201022B), Science and Technology Development Fund Key Project of Nanjing Medical University (No. 2012NJMU001), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Conflict of interest

The authors declare no potential conflict of interests with respect to the authorship and/or publication of this paper.

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Authors and Affiliations

  1. Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210029, China

    Li Guo, Yang Zhao, Sheng Yang, Min Cai & Feng Chen

  2. State Key Laboratory of Reproductive Medicine, Department of Hygienic Analysis and Detection, School of Public Health, Nanjing Medical University, Nanjing, 210029, China

    Qian Wu

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  1. Li Guo
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  2. Yang Zhao
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  3. Sheng Yang
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  4. Min Cai
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Correspondence to Qian Wu or Feng Chen.

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11033_2012_2277_MOESM1_ESM.tif

Figure S1. Trends in expression of abundantly expressed miRNAs (at least 0.30%) in the 7 paired tumor and adjacent normal samples. (A) Trends of miRNA expression in 7 tumor tissue samples; (B) Trends of miRNA expression in 7 normal tissue samples. Except for several specific miRNAs, the rest of the miRNAs exhibited lower expression levels. Supplementary material 1 (TIFF 848 kb)

11033_2012_2277_MOESM2_ESM.tif

Figure S2. Distribution of abundantly expressed miRNA species between tumor and adjacent normal samples. P-T: indicates patient-tumor sample, P-N: indicates patient-adjacent normal sample, All-T: indicates all tumor samples (from 7 patients), All-N: indicates all adjacent normal samples (from 7 patients). Supplementary material 2 (TIFF 2578 kb)

11033_2012_2277_MOESM3_ESM.tif

Figure S3. Abundantly expressed miRNAs and their dynamic expression profiles. (A) Distribution of abundantly expressed miRNA in mixed tumor/adjacent normal tissues and serum normal/tumor samples. Relative expression levels of these miRNAs were at least 0.30% in a sample. T-T: indicates mixed tumor tissue sample (from 7 patients); T-N: indicates mixed adjacent normal tissue sample (from 7 patients); S-T: indicates mixed serum tumor sample; S-N: indicates mixed serum normal sample; (B) Fold change values (log2) of the common miRNA species based on the normal sample. Aberrantly expressed miRNAs (fold change value is more than 1.50, or less than -1.50) were highlighted in yellow (up-regulation) and green (down-regulation) background. Supplementary material 3 (TIFF 2376 kb)

11033_2012_2277_MOESM4_ESM.tif

Figure S4. Significantly dysregulated miRNAs detected in at least two patients. (A) There are 3 commonly up-regulated miRNAs in three patients; (B) There are 2 commonly up-regulated miRNAs in two patients; (C) There are 10 commonly down-regulated miRNAs in two patients; (D) 18 miRNAs detected in two patients exhibited opposite dysregulation patterns. Supplementary material 4 (TIFF 817 kb)

11033_2012_2277_MOESM5_ESM.tif

Figure S5. Principal component analysis (PCA) of all samples based on abundantly expressed miRNAs (more than 1.00% in a sample). (A) Based on relative expression levels; (B) Based on normalized data of relative expression levels. All samples were color coded in blue (tumor samples) and red (normal samples). Supplementary material 5 (TIFF 175 kb)

Supplementary material 6 (DOCX 29 kb)

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Guo, L., Zhao, Y., Yang, S. et al. Genome-wide screen for aberrantly expressed miRNAs reveals miRNA profile signature in breast cancer. Mol Biol Rep 40, 2175–2186 (2013). https://doi.org/10.1007/s11033-012-2277-5

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