An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

• Published in: Cell Vol. 147; no. 2; pp. 370 - 381
• Main Authors: Sumazin, Pavel, Yang, Xuerui, Chiu, Hua-Sheng, Chung, Wei-Jen, Iyer, Archana, Llobet-Navas, David, Rajbhandari, Presha, Bansal, Mukesh, Guarnieri, Paolo, Silva, Jose, Califano, Andrea
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 14.10.2011
• Subjects: cell growth; gene expression; Gene Expression Regulation, Neoplastic; genes; Glioblastoma - genetics; Glioblastoma - metabolism; Humans; loci; microRNA; MicroRNAs - metabolism; Multivariate Analysis; neoplasm cells; Oncogenes; PTEN Phosphohydrolase - genetics; RNA Interference; small interfering RNA
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2011.09.041

By analyzing gene expression data in glioblastoma in combination with matched microRNA profiles, we have uncovered a posttranscriptional regulation layer of surprising magnitude, comprising more than 248,000 microRNA (miR)-mediated interactions. These include ∼7,000 genes whose transcripts act as miR “sponges” and 148 genes that act through alternative, nonsponge interactions. Biochemical analyses in cell lines confirmed that this network regulates established drivers of tumor initiation and subtype implementation, including PTEN, PDGFRA, RB1, VEGFA, STAT3, and RUNX1, suggesting that these interactions mediate crosstalk between canonical oncogenic pathways. siRNA silencing of 13 miR-mediated PTEN regulators, whose locus deletions are predictive of PTEN expression variability, was sufficient to downregulate PTEN in a 3′UTR-dependent manner and to increase tumor cell growth rates. Thus, miR-mediated interactions provide a mechanistic, experimentally validated rationale for the loss of PTEN expression in a large number of glioma samples with an intact PTEN locus. [Display omitted] ► Computational inference reveals a network of miR-mediated interactions in glioblastoma ► These interactions regulate thousands of genes, including oncogenes and tumor suppressors ► These interactions regulate miR targets without affecting miR expression ► These interactions enable crosstalk between established oncogenic pathways Computational inference uncovers a massive RNA-RNA interaction network in glioblastoma, which is shown to regulate established tumor drivers, such as PTEN, by modulating microRNA availability.