Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

Miriam R. Aure, Suvi Katri Leivonen, Thomas Fleischer, Qian Zhu, Jens Overgaard, Jan Alsner, Trine Tramm, Riku Louhimo, Grethe I.G. Alnæs, Merja Perälä, Florence Busato, Nizar Touleimat, Jörg Tost, Anne Lise Børresen-Dale, Sampsa Hautaniemi, Olga G. Troyanskaya, Ole C. Lingjærde, Kristine K. Sahlberg, Vessela N. Kristensen

Research output: Contribution to journalArticlepeer-review

76 Scopus citations


Background: The global effect of copy number and epigenetic alterations on miRNA expression in cancer is poorly understood. In the present study, we integrate genome-wide DNA methylation, copy number and miRNA expression and identify genetic mechanisms underlying miRNA dysregulation in breast cancer.Results: We identify 70 miRNAs whose expression was associated with alterations in copy number or methylation, or both. Among these, five miRNA families are represented. Interestingly, the members of these families are encoded on different chromosomes and are complementarily altered by gain or hypomethylation across the patients. In an independent breast cancer cohort of 123 patients, 41 of the 70 miRNAs were confirmed with respect to aberration pattern and association to expression. In vitro functional experiments were performed in breast cancer cell lines with miRNA mimics to evaluate the phenotype of the replicated miRNAs. let-7e-3p, which in tumors is found associated with hypermethylation, is shown to induce apoptosis and reduce cell viability, and low let-7e-3p expression is associated with poorer prognosis. The overexpression of three other miRNAs associated with copy number gain, miR-21-3p, miR-148b-3p and miR-151a-5p, increases proliferation of breast cancer cell lines. In addition, miR-151a-5p enhances the levels of phosphorylated AKT protein.Conclusions: Our data provide novel evidence of the mechanisms behind miRNA dysregulation in breast cancer. The study contributes to the understanding of how methylation and copy number alterations influence miRNA expression, emphasizing miRNA functionality through redundant encoding, and suggests novel miRNAs important in breast cancer.

Original languageEnglish (US)
Article numberR126
JournalGenome biology
Issue number11
StatePublished - Nov 20 2013

All Science Journal Classification (ASJC) codes

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Cell Biology


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