Functional profiling of precursor MicroRNAs identifies MicroRNAs essential for glioma proliferation

PLoS One. 2013;8(4):e60930. doi: 10.1371/journal.pone.0060930. Epub 2013 Apr 5.

Abstract

Cancer initiation and progression involve microRNAs that can function like tumor suppressors and oncogenes. The functional significance of most miRNAs is currently unknown. To determine systematically which microRNAs are essential for glioma growth, we screened a precursor microRNA library in three human glioblastoma and one astroglial cell line model systems. The most prominent and consistent cell proliferation-reducing hits were validated in secondary screening with an additional apoptosis endpoint. The functional screening data were integrated in the miRNA expression data to find underexpressed true functional tumor suppressor miRNAs. In addition, we used miRNA-target gene predictions and combined siRNA functional screening data to find the most probable miRNA-target gene pairs with a similar functional effect on proliferation. Nine novel functional miRNAs (hsa-miR-129, -136, -145, -155, -181b, -342-5p, -342-3p, -376a/b) in GBM cell lines were validated for their importance in glioma cell growth, and similar effects for six target genes (ROCK1, RHOA, MET, CSF1R, EIF2AK1, FGF7) of these miRNAs were shown functionally. The clinical significance of the functional hits was validated in miRNA expression data from the TCGA glioblastoma multiforme (GBM) tumor cohort. Five tumor suppressor miRNAs (hsa-miR-136, -145, -342, -129, -376a) showed significant underexpression in clinical GBM tumor samples from the TCGA GBM cohort further supporting the role of these miRNAs in vivo. Most importantly, higher hsa-miR-145 expression in GBM tumors yielded significantly better survival (p<0.005) in a subset of patients thus validating it as a genuine tumor suppressor miRNA. This systematic functional profiling provides important new knowledge about functionally relevant miRNAs in GBM biology and may offer new targets for treating glioma.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Proliferation
  • Gene Expression Profiling*
  • Glioblastoma / genetics*
  • Glioblastoma / pathology*
  • Humans
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism*
  • Neoplastic Cells, Circulating

Substances

  • MicroRNAs

Grants and funding

This work was supported by the Academy of Finland (Translational Genome-Scale Biology Center of Excellence and Center of Excellence in Cancer Genetics Research), Finnish Cancer Organisations, the Sigrid Jusélius foundation, EU-FP6 project RIGHT (LSHB-CT-2004-005276), and Finnish Graduate School in Computational Sciences (PC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.