Cross-Species Functional Genomic Analysis Identifies Resistance Genes of the Histone Deacetylase Inhibitor Valproic Acid
Figure 3
Conserved pathways contribute to VPA resistance.
A) The human homologs/orthologs of data from all screens were combined in an in silico approach to extract and predict common functionalities and components. Proteins identified in our datasets (red), as well as direct interactors and indirect interactors (black) mediated via one neighbor extracted by the FunCoup browser, were imported into Cytoscape which returned five clusters of enriched process which were manually grouped (grey shade) to illustrate that “APC-dependent proteasomal ubiquitin-dependent protein degradation” and “Response to unfolded protein” are the major conserved processes responding to VPA. In addition, “Regulation of TGFβ receptor signaling” and “Transport” are also functionally important in providing resistance to VPA. The scale depicts color representation of significance by Benjamini-Hochberg correction, where white nodes are not significant, yellow p<0.05 and orange p<7×10−7. B) Protein interaction network reveal conserved hubs that promote VPA resistance. Data from all screens were combined in silico and the functional interaction network among the common proteins (diamonds) were extracted using FunCoup. ACTB, HSC70, and TUBA1B (red) were in the primary list whereas MAPKAPK2, HSP90AA2 and HSP90AB1 (black) were identified in all approaches as interactors. ACTB, HSC70, HSP90AA2, HSP90AB1 and TUBA1B represent evolutionary conserved nodes providing resistance to VPA. C) VPA (1 mM) was combined with inhibitors of tubulin (vincristine (VCR), 1 nM) or HSP90 (geldanamycin (GA), 5 nM) in MOLM-13 AML cells and investigated for effects on apoptosis measured by Hoechst staining after 48 hours of treatment. Arrows indicate fragmented and condensed nuclei. Scale bar = 10 µm. Combinations of 1 mM VPA and 1 nM vincristine (D), 2 mM VPA and inhibitor of actin polymerization cytochalasin B (E), 1 mM VPA and 5 nM geldanamycin (F), and 0.2 mM SAHA and 5 nM geldanamycin (G) all show statistically significant synergism of drug interaction, two-way ANOVA, * p<0.05, ** p<0.001, *** p<0.0001. Error bars represent standard error of mean (SEM).