Histone deacetylase inhibitors are currently being evaluated for their therapeutic potential and have shown considerable promise as adjuvant therapies for a number of cancers. This study compared the effects of 2 hydroxamic acid based inhibitors, CG-1521 and SAHA, on gene expression, cell cycle and cell death in MCF-7 human breast cancer cells. Both compounds show a dose- and time-dependent effect on cell number (evaluated using crystal violet), however CG-1521 exerts its effects significantly earlier than SAHA, and CG-1521 induces apoptosis (assessed by Apo-BrdU staining and flow cytometry) more rapidly than SAHA. qPCR of cell cycle regulatory and apoptotic genes shows that CG-1521 and SAHA modulate similar cohorts of p53-responsive genes, however, the levels of induction and the timing of the induction differs significantly between the 2 inhibitors. In particular SAHA downregulates cell cycle-associated genes that modulate the G1/S transition (including cyclin D1 and cdc25a) and the G2/M transition [cyclin B1, Plk1, Stk6 (serine-threonine kinase 6, Aurora kinase A) and Kntc2] more significantly than CG-1521. In contrast, CG-1521 significantly induces the expression of several p53 target genes associated with apoptosis including Bnip3/Bnip3L, p21/p21B and Gdf15. The differential levels of gene induction provide molecular evidence of both cell cycle arrest and apoptosis, and suggest a molecular mechanism that explains the difference in the biological effects of the 2 histone deacetylase inhibitors.

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