Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma

Abstract

Background The sensitivity of MYC amplified medulloblastoma to class I HDAC inhibition has been shown previously, however understanding the underlying molecular mechanism is crucial for selection of effective HDAC inhibitors for clinical use. The aim of this study was to investigate the direct molecular interaction of MYC and the class I HDAC2, and the impact of class I HDAC inhibition on MYC function. Methods Co-immunoprecipitation and mass spectrometry was used to determine the co-localization of MYC and HDAC2. ChIP-sequencing and gene expression profiling was used to analyze the co- localization of MYC and HDAC2 on DNA and the impact on transcriptional activity in primary tumors and a MYC amplified cell line treated with the class I HDAC inhibitor entinostat. The effect on MYC was investigated by quantitative RT-PCR, Western blot and immunofluorescence. Results HDAC2 is a cofactor of MYC in MYC amplified medulloblastoma. The MYC-HDAC2 complex is bound to genes defining the MYC-dependent transcriptional profile. Class I HDAC inhibition leads to stabilization and reduced DNA-binding of MYC protein inducing a down-regulation of MYC activated genes (MAGs) and up-regulation of MYC repressed genes (MRGs). MAGs and MRGs are characterized by opposing biological functions and by distinct E-box distribution. Conclusions Our data elucidates the molecular interaction of MYC and HDAC2 and support a model in which inhibition of class I HDACs directly targets MYC´s trans-activating and trans-repressing function.

A synergistic interaction between HDAC- and PARP inhibitors in childhood tumors with chromothripsis

“…As MYC and MYCN are frequently amplified and overexpressed in the three tumor types investigated in this screen, it will be important to further investigate the precise role of these factors in the treatment response. The HDACi entinostat was shown to inhibit MYC transcriptional activity in MYC amplified MB 21 , in line with the downregulation of MYC target genes observed here upon combination treatment. Interestingly, a previous study identified HDAC and Pi3K antagonists to inhibit MYC-driven medulloblastoma 19 .…”

The Role of Post-Translational Acetylation and Deacetylation of Signaling Proteins and Transcription Factors after Cerebral Ischemia: Facts and Hypotheses

“…However, inhibitors of HDAC, but not sirtuins, increased the acetylation of c-Myc at lysine 323 and inhibited tumorigenesis [ 88 ], which promoted the association of c-Myc with Max, a partner required for c-Myc activation. HDAC inhibitors downregulated c-Myc by blocking GSK-3 phosphorylation and exhibited synergistic cytotoxic and c-Myc-suppressive effects ( Figure 4 ) [ 89 ]. HDAC3 also deacetylated c-Myc at lysine 323 in cholangiocarcinoma cells, which protected the protein from ubiquitin-dependent proteolysis [ 90 ].…”

Distribution and vulnerability of transcriptional outputs across the genome in Myc-amplified medulloblastoma cells

“…Genomics Browser (IGV 2.8.9, released January 2020) was used for displaying and visualizing next generational sequencing data. For Myc's binding to histone genes in MB tumors, ChIP-seq data were obtained from the recently published study (GSE143386: GSM4257878_MB1, GSM4257882_MB2 and GSM4257886_MB3) 30 . For all images illustrating the nascent RNA, the numbers of reads uniquely mapped to the genome were used for data range normalization when the IGV images were generated.…”

“…4b). To further define the regulatory role of Myc in the expression of the histone genes, we analyzed previously reported ChIP-seq data in Myc-driven MBs 30 . The analysis revealed Myc's binding to all histone genes that were detected in the nascent RNA-seq (Fig.…”