Based on these observations we surmise that similar HDACI induced gene research use only networks were uncovered by IPA and KEGG analyses. A putative involvement of MAPK pathways in the action of pan HDAC inhibitors The network analyses of genes that were differentially regulated by CBHA and TSA, regardless of whether it was done by IPA or KEGG programs, strongly predicted a role of PTEN PI3K AKT PKB and MAPK signaling pathways in the actions of HDACIs. We reported earlier that both CBHA and TSA potently induced the expres sion of PTEN and concomitant reduction in PI3K and AKT phosphorylation in H9c2 cells as well as in the in tact heart. To test a potential role of MAP kinases, we extracted proteins from H9c2 cells incubated with CBHA or TSA for various time intervals and assessed the steady state levels of total and phosphorylated ERK, JNK and p38 MAPK.
As shown in Figure 11, an expos ure to TSA for 4h led to a reduced phosphorylation of ERK and its phosphorylation remained inhibited until 24h. TSA treatment also significantly suppressed phosphorylation of p38 as early as 2h. Finally, an exposure of H9c2 cells to CBHA resulted in a reduction of pERK at 4h, while the levels of p p38 kinase were not significantly affected by CBHA. The temporal changes in the regulation of JNK in response to CBHA or TSA were inconclusive. Finally, it should be noted that neither TSA nor CBHA altered the steady state levels of total ERK or p38 kinases.
Frequency of putative transcription factor binding sites in differentially expressed genes in response to CBHA and TSA With an aim to elucidate potentially common pathways involved in the induction of genes by CBHA and TSA, we extended gene network analyses by an in silico exam ination of transcription factor binding sites in the promoters of DEGs. We explored 1 kb of DNA upstream of transcription start site of all differentially expressed genes by CORE TF, a web based program that identifies dominant TFBS. As shown in Table 5, in DEGs induced by CBHA at 6 and 24h, the topmost transcrip tional factor motifs were those of AP2, CHCH, E2F1, EGR2 and ETF. An over representation of AP2, CHCH, E2F1, EGR2 and ETF was also seen in TSA treated cells, additionally, the promoters of the TSA induced DEGs expressed zinc finger containing transcription factors. Finally, NF Y specific motifs were overrepresented in DEGs induced by TSA at 24h.
The preponderance of E2F1, EGR2, Sp1 and KROX tran scription factor binding sites in the DEGs induced by ei ther pan HDAC inhibitor was consistent with an ability of these transcription factors to regulate genes involved in cell proliferation and apoptosis. The members of the E2F family, that bind to RB1, also Dacomitinib play a key role in regulating G to S transition, similarly, NF Y has a fun damental role in the expression of genes that regulate G2 M phase of the cell cycle.