Downregulation of Homologous Recombination DNA Repair Genes by HDAC Inhibition in Prostate Cancer Is Mediated through the E2F1 Transcription Factor

Abstract

BackgroundHistone deacetylase inhibitors (HDACis) re-express silenced tumor suppressor genes and are currently undergoing clinical trials. Although HDACis have been known to induce gene expression, an equal number of genes are downregulated upon HDAC inhibition. The mechanism behind this downregulation remains unclear. Here we provide evidence that several DNA repair genes are downregulated by HDAC inhibition and provide a mechanism involving the E2F1 transcription factor in the process.Methodology/Principal FindingsApplying Analysis of Functional Annotation (AFA) on microarray data of prostate cancer cells treated with HDACis, we found a number of genes of the DNA damage response and repair pathways are downregulated by HDACis. AFA revealed enrichment of homologous recombination (HR) DNA repair genes of the BRCA1 pathway, as well as genes regulated by the E2F1 transcription factor. Prostate cancer cells demonstrated a decreased DNA repair capacity and an increased sensitization to chemical- and radio-DNA damaging agents upon HDAC inhibition. Recruitment of key HR repair proteins to the site of DNA damage, as well as HR repair capacity was compromised upon HDACi treatment. Based on our AFA data, we hypothesized that the E2F transcription factors may play a role in the downregulation of key repair genes upon HDAC inhibition in prostate cancer cells. ChIP analysis and luciferase assays reveal that the downregulation of key repair genes is mediated through decreased recruitment of the E2F1 transcription factor and not through active repression by repressive E2Fs.Conclusions/SignificanceOur study indicates that several genes in the DNA repair pathway are affected upon HDAC inhibition. Downregulation of the repair genes is on account of a decrease in amount and promoter recruitment of the E2F1 transcription factor. Since HDAC inhibition affects several pathways that could potentially have an impact on DNA repair, compromised DNA repair upon HDAC inhibition could also be attributed to several other pathways besides the ones investigated in this study. However, our study does provide insights into the mechanism that governs downregulation of HR DNA repair genes upon HDAC inhibition, which can lead to rationale usage of HDACis in the clinics.

Synergistic Loss of Prostate Cancer Cell Viability by Coinhibition of HDAC and PARP

“…proteins involved in HR repair of DSBs, BRCA1, and RAD51, were downregulated by both inhibitors. This is consistent with several studies that demonstrated HDAC inhibitors suppress HR gene expression through the E2F1 transcriptional regulator (17), translational repression via miRNAs such as miR182 (34), as well as posttranslational degradation through hyperacetylation of Hsp90 (35). Nonetheless, antineoplastic mechanism of action for HDAC inhibitors has not been well elucidated, and due to their broad range of possible targets, it is likely the SAHA may have affected the function of other proteins involved in DNA damage response.…”

“…HDACs regulate gene expression by modifying the chromatin structure as well as regulating the function of nonhistone proteins (15). HDAC inhibition has been reported to downregulate the expression of proteins involved in HR leading to impaired repair of DSBs, i.e., increase "BRCAness" in various types of cancers (16)(17)(18)(19). We hypothesize that HDAC inhibition by SAHA can modulate the expression of proteins involved in DSB repair and abrogate DNA damage response in prostate cancer cells, thereby sensitizing them to PARP inhibition.…”

Expression of Leukemia-Associated Fusion Proteins Increases Sensitivity to Histone Deacetylase Inhibitor–Induced DNA Damage and Apoptosis

“…Expression of LAFPs was previously shown to downregulate a number of BER genes (8). HDIs have been shown to downregulate a number of DNA repair enzymes including enzymes implicated in BER and DSB repair (14,40,41). Therefore, we sought to investigate the effect of vorinostat on these same genes in the presence or absence of PLZF-RARa or AML1-ETO.…”

Global Gene Profiling of Laser-Captured Pollen Mother Cells Indicates Molecular Pathways and Gene Subfamilies Involved in Rice Meiosis

“…Downregulation of HDA703 by artificial miRNA reduced rice fertility (Hu et al, 2009). In mammals, HDAC inhibition down-regulates homologous recombination DNA repair pathways (Kachhap et al, 2010).…”