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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

1
IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, Salzburg 5020, Austria
2
Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, Salzburg 5020, Austria
3
Cancer Cluster Salzburg, Salzburg 5020, Austria
4
Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
5
Department of Pathology, Paracelsus Medical University Salzburg, Salzburg 5020, Austria
6
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]   |  

Abstract

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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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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