Figure 1.
Heatmap of miRNA profile in 6 cell lines.
(A). The expression values of 380 DEmiRs were measured and hierarchical clustering was performed. The expression profile of HepG2 and Hep293TT were clustered with Daoy. RD-ES and MG-63 are grouped together with SH-SY5Y. Differentially expressed miRNAs (B). Twenty-six miRNAs with at least 2-fold change in 4 or more cell-lines were selected. Twenty-three miRNAs were up regulated and 3 were down regulated.
Figure 2.
(A). The p53 pathway that includes 8 signaling components as defined by KEGG was highly regulated by the CSC associated DEmiRs. Five of the 26 DEmiRs were implicated in this pathway, hsa-miR-21-5p, hsa-miR-135b, hsa-miR-29, hsa-miR-655, hsa-miR-494. TGF-beta pathway of KEGG (B). The TGF-beta pathway was also regulated by the CSC associated DEmiRs. Receptor TGFBR1 was regulated by hsa-miR-101-3p, and receptor TGFBR2 was regulated by hsa-miR-21-5p, and hsa-miR-519a-3p. The receptor BMPR2 was regulated by hsa-miR-101-3p, hsa-miR-21-5p, hsa-miR-181c-5p, and hsa-miR-494. Nodal type II receptor kinase and receptor ACVR2B were also regulated by hsa-miR-101-3p.
Table 1.
CSC associated DEmiRs regulated KEGG pathways.
Table 2.
CSC associated DEmiRs regulated BioCarta pathways.
Table 3.
CSC associated DEmiRs regulated Biological Processes (Gene Ontology Terms).
Figure 3.
hsa-miR-21-5p knockdown on the ALDHBR fraction in Daoy.
(A). Approximately a two-fold reduction in the fraction enriched for stem-like cells was observed in the hsa-miR-21-5p knockdown. Data shown is representative of three independent experiments. hsa-miR-135b-5p inhibition on the ability to form neurospheres in SK-N-NE(2) (B). An impairment of sphere formation was seen in the SK-N-BE(2) hsa-miR-135b-5p stable knockdown. hsa-miR-135b-5p KD1, KD2 and KD3 were from the same clone. Data represents three independent experiments, presented as the mean ± SEM.
Table 4.
CSC associated DEmiRs and targeted pathways that do not meet following criterion as described in the Results Section: Percentage of miRNA target genes in a gene set is less than 10% or less than 3 genes are regulated by DEmiRs per pathway.