Figure 5.
Overexpression of candidate proneural miRNAs in neurospheres drives expression changes consistent with their predicted role in tumors. (A) Expression changes after miR-124 overexpression in a proneural (PDGFRA-amplified) neurosphere were concordant with miR-124 associated tumor versus normal expression changes, where miR-124 is underexpressed. Targets of miR-124 that were downregulated in the neurosphere model and genes those were upregulated after miR-124 transfection are upregulated and downregulated, respectively, in TCGA proneural samples. These results suggest that overexpression of miR-124 in neurospheres partially reverses the expression changes in proneural tumors. (B) miR-132 also shows expression concordance in proneural tumors and miR-132 overexpression in neurospheres. (C) Common regulator miR-124 and proneural-specific regulator miR-132 show concordant gene expression changes between transfection in neurosphere and TCGA proneural samples. Two control microRNAs (miR-380 and miR-448), both downregulated in proneural samples but not selected in the regression analysis, do not show this concordance. A final tested miRNA, miR-443, was downregulated in proneural samples and chosen as a regulator by sample-based regression models but not the group lasso method and does not show significant concordance between expression changes (Supplementary Table 9). (D) Cell proliferation analysis demonstrates a significant decrease in number of cells in S phase and significant increase in number of cells in G0/G1 phase in miR-124 transfection compared with negative controls. These results are consistent with gene ontology analysis of miR-124 transfection data. Values represent mean±standard deviation of three replicate experiments (*P<2e−5, t-test). (E) Examination of identified regulators and existing literature suggests a proneural-specific core regulatory network. REST, a repressor of neural genes in non-neuronal cells, is known to be upregulated in brain tumors. YY1, inferred as an activator in proneural tumors, is a known activator of REST. Upregulation of REST may lead to downregulation of the miRNAs miR-124 (a predicted regulator in all subtypes) and miR-132 (a predicted regulator specific to proneural subtype). Downregulation of miR-124 and miR-132 may contribute to inhibition of differentiation and proliferation in tumors. Source data is available for this figure in the Supplementary Information.
