How breast cancer cells survive the epigenetic disruption caused by histone deacetylase inhibitors

Histone deacetylase inhibitors (HDACi) have had a patchy history as anti-cancer treatments, only showing efficacy against specific haematological tumours. They have as yet shown no benefit when used in solid tumours. Previous work in our lab has shown that a specific transcriptional mechanism enables some cells to survive in the presence of an HDACi – a response termed the HDACi survival response. The coordinated change in the cell’s gene expression pattern allows it to survive the epigenetic disruption caused by global protein hyperacetylation. The work reported here sets out to identify the genes and signalling pathways that were crucial in allowing cells to survive the toxic effects of HDAC inhibition and explore the extent to which these key genes are mutated in cancer. This was done by analysing genes responding rapidly following SAHA (suberoylanilide hydroxamic acid) treatment of an HDACi sensitive (MDA-MB231) and more HDACi resistant (MCF7) cell-line. Factors predicted to drive this response were selected and their role validated through knockdown. This work identified key differences between our cell-lines. The knockdown of ATF4 and CREB3L4 increased the HDACi sensitivity of MCF7 cells, while POU2F2, ATF4 and ATF5 knockdown further enhanced the sensitivity of MDA-MB231 cells. Reduced Representation Bisulfite Sequencing (RRBS) analysis showed that there was no evidence DNA methylation was involved in the early transcriptional response following HDACi treatment. However, it did show that HDACi inhibition induced a dynamic change in methylation in both cell-lines. The CBioPortal database was used to compare our cell-lines to a breast cancer patient cohort. This analysis confirmed that MCF7 and MDA-MB231 cells were representative of their luminal A and triple-negative molecular subtypes in terms of expression of the key genes we have identified. Based on this and our experimental data, we hypothesised that triple-negative tumours may be more receptive to these drugs. Additionally, the genes selected for analysis appeared to be differentially expressed by subtype. Therefore, transcriptional profiles could potentially be used to indicate a subpopulation of triple-negative tumours more likely to respond to HDAC inhibition.