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Int. J. Mol. Sci. 2016, 17(2), 156; doi:10.3390/ijms17020156

miR-16-5p Is a Stably-Expressed Housekeeping MicroRNA in Breast Cancer Tissues from Primary Tumors and from Metastatic Sites

IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, Salzburg 5020, Austria
Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, Salzburg 5020, Austria
Cancer Cluster Salzburg, Salzburg 5020, Austria
Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
Department of Pathology, Paracelsus Medical University Salzburg, Salzburg 5020, Austria
Department of Radiotherapy, Paracelsus Medical University Salzburg, Salzburg 5020, Austria
These authors contributed equally to this work.
Author to whom correspondence should be addressed.
Academic Editor: Martin Pichler
Received: 30 November 2015 / Revised: 20 January 2016 / Accepted: 21 January 2016 / Published: 26 January 2016
(This article belongs to the Collection Regulation by Non-Coding RNAs)
View Full-Text   |   Download PDF [552 KB, uploaded 26 January 2016]   |  


For quantitative microRNA analyses in formalin-fixed paraffin-embedded (FFPE) tissue, expression levels have to be normalized to endogenous controls. To investigate the most stably-expressed microRNAs in breast cancer and its surrounding tissue, we used tumor samples from primary tumors and from metastatic sites. MiRNA profiling using TaqMan® Array Human MicroRNA Cards, enabling quantification of 754 unique human miRNAs, was performed in FFPE specimens from 58 patients with metastatic breast cancer. Forty-two (72%) samples were collected from primary tumors and 16 (28%) from metastases. In a cross-platform analysis of a validation cohort of 32 FFPE samples from patients with early breast cancer genome-wide microRNA expression analysis using SurePrintG3 miRNA (8 × 60 K)® microarrays from Agilent® was performed. Eleven microRNAs could be detected in all samples analyzed. Based on NormFinder and geNorm stability values and the high correlation (rho ≥ 0.8) with the median of all measured microRNAs, miR-16-5p, miR-29a-3p, miR-126-3p, and miR-222-3p are suitable single gene housekeeper candidates. In the cross-platform validation, 29 human microRNAs were strongly expressed (mean log2-intensity > 10) and 21 of these microRNAs including miR-16-5p and miR-29a-3p were also stably expressed (CV < 5%). Thus, miR-16-5p and miR-29a-3p are both strong housekeeper candidates. Their Normfinder stability values calculated across the primary tumor and metastases subgroup indicate that miR-29a-3p can be considered as the strongest housekeeper in a cohort with mainly samples from primary tumors, whereas miR-16-5p might perform better in a metastatic sample enriched cohort. View Full-Text
Keywords: miR-16; miR-16-5p; microRNA; endogenous control; housekeeper; control; breast cancer miR-16; miR-16-5p; microRNA; endogenous control; housekeeper; control; breast cancer

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Rinnerthaler, G.; Hackl, H.; Gampenrieder, S.P.; Hamacher, F.; Hufnagl, C.; Hauser-Kronberger, C.; Zehentmayr, F.; Fastner, G.; Sedlmayer, F.; Mlineritsch, B.; Greil, R. miR-16-5p Is a Stably-Expressed Housekeeping MicroRNA in Breast Cancer Tissues from Primary Tumors and from Metastatic Sites. Int. J. Mol. Sci. 2016, 17, 156.

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