CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma

by Selleckchem | Aug 22 2023

Diffuse large B-cell lymphoma (DLBCL) exhibits significant genetic heterogeneity which contributes to drug resistance, necessitating development of novel therapeutic approaches. Pharmacological inhibitors of cyclin-dependent kinases (CDK) demonstrated pre-clinical activity in DLBCL, however many stalled in clinical development. Here we show that AZD4573, a selective inhibitor of CDK9, restricted growth of DLBCL cells. CDK9 inhibition (CDK9i) resulted in rapid changes in the transcriptome and proteome, with downmodulation of multiple oncoproteins (eg, MYC, Mcl-1, JunB, PIM3) and deregulation of phosphoinotiside-3 kinase (PI3K) and senescence pathways. Following initial transcriptional repression due to RNAPII pausing, we observed transcriptional recovery of several oncogenes, including MYC and PIM3. ATAC-Seq and ChIP-Seq experiments revealed that CDK9i induced epigenetic remodeling with bi-directional changes in chromatin accessibility, suppressed promoter activation and led to sustained reprograming of the super-enhancer landscape. A CRISPR library screen suggested that SE-associated genes in the Mediator complex, as well as AKT1, confer resistance to CDK9i. Consistent with this, sgRNA-mediated knockout of MED12 sensitized cells to CDK9i. Informed by our mechanistic findings, we combined AZD4573 with either PIM kinase or PI3K inhibitors. Both combinations decreased proliferation and induced apoptosis in DLBCL and primary lymphoma cells in vitro as well as resulted in delayed tumor progression and extended survival of mice xenografted with DLBCL in vivo. Thus, CDK9i induces reprogramming of the epigenetic landscape, and super-enhancer driven recovery of select oncogenes may contribute to resistance to CDK9i. PIM and PI3K represent potential targets to circumvent resistance to CDK9i in the heterogeneous landscape of DLBCL.

Comments:

The passage you provided describes a study on diffuse large B-cell lymphoma (DLBCL) and the potential use of a selective inhibitor of cyclin-dependent kinase 9 (CDK9) called AZD4573 as a therapeutic approach. DLBCL is known for its genetic heterogeneity and resistance to certain drugs, so new treatment strategies are needed.

The researchers found that AZD4573 inhibited the growth of DLBCL cells. CDK9 inhibition resulted in rapid changes in both the transcriptome (the set of all RNA molecules produced in a cell) and proteome (the set of all proteins produced in a cell). Multiple oncoproteins, such as MYC, Mcl-1, JunB, and PIM3, were downregulated, and the phosphoinotiside-3 kinase (PI3K) and senescence pathways were deregulated.

After the initial transcriptional repression caused by CDK9 inhibition, the researchers observed a subsequent transcriptional recovery of several oncogenes, including MYC and PIM3. Through ATAC-Seq and ChIP-Seq experiments, they discovered that CDK9 inhibition induced epigenetic remodeling, resulting in bidirectional changes in chromatin accessibility. This led to suppressed promoter activation and sustained reprogramming of the super-enhancer landscape. Super-enhancers are regions of the genome that control the expression of critical genes, including oncogenes.

To investigate potential resistance mechanisms, the researchers performed a CRISPR library screen and found that genes associated with super-enhancers in the Mediator complex, as well as AKT1, may confer resistance to CDK9 inhibition. To validate this, they performed sgRNA-mediated knockout of MED12, which sensitized cells to CDK9 inhibition.

Based on their mechanistic findings, the researchers combined AZD4573 with either PIM kinase or PI3K inhibitors. Both combinations showed decreased proliferation and induced apoptosis in DLBCL and primary lymphoma cells in vitro. Furthermore, in mice xenografted with DLBCL, these combinations resulted in delayed tumor progression and extended survival.

Overall, the study highlights the reprogramming of the epigenetic landscape by CDK9 inhibition and the super-enhancer-driven recovery of specific oncogenes, which may contribute to resistance to CDK9 inhibitors in the heterogeneous landscape of DLBCL. The researchers propose that targeting PIM and PI3K pathways could be potential strategies to overcome resistance to CDK9 inhibitors in DLBCL.