CDK9 inhibition with AZD4573 in DLBCL

We report the effects of CDK9 inhibition (AZD4573) on the epigenetic landscape in Diffuse Large B-cell Lymphoma (DLBCL). This study utilized chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq) to assess genome-wide post-translational histone modifications (H3K27ac and H3K4me3) and DNA occupancy of transcriptional proteins (RNAPII and BRD4) in two DLBCL cell lines, OCI-LY3 and VAL, treated with the CDK9 inhibitor AZD4573 (30 nM). Cells were treated for 0, 3 and 8 hours prior to harvest. After 8-hour exposure, drug was washed out and cells were harvested after 24 hours. We found that CDK9 inhibition led to an increase in RNAPII promoter proximal pausing, and increase in BRD4 enrichment on the promoter, and a decrease in promoter H3K4me3. Treatment induced reprograming of the super-enhancer landscape including loss of super-enhancers next to genes in oncogenic pathways. Overall design: Two DLBCL cell lines, OCI-LY3 (GC-DLBCL) and VAL (ABC-DLBCL), were treated with AZD4573 (30 nM) for 0, 3 and 8 hours prior to harvest. After 8-hour exposure, drug was washed out and cells were harvested after 24 hours. Samples were subjected to ChIP-sequencing. OCI-LY3 and VAL cells were immunoprecipitated for H3K4me3 and H3K27ac, and OCI-LY3 cells were additionally immunoprecipitated for RBP1 and BRD4. As controls, OCI-LY3 and VAL cells were immunoprecipitated for IgG, and samples of input DNA (no immunoprecipitation) were additionally included.