CDK9 inhibition strategy defines distinct sets of target genes

BMC Research Notes

Xavier Graña²  Judit Garriga¹ 

[1]Fels Institute for Cancer Research and Molecular Biology, AHP bldg., room 308, 3307 North Broad St., Philadelphia, PA 19140, USA

[2]Department of Biochemistry, Temple University School of Medicine, 3307 North Broad St., Philadelphia, PA 19140, USA

关键词: Control of gene expression;    CDKs;    RNA polymerase II;    CDK9;    Transcription;   

Others  :  1132757
DOI  :  10.1186/1756-0500-7-301

 received in 2013-12-13, accepted in 2014-05-08,  发布年份 2014

【 摘 要 】

Background

CDK9 is the catalytic subunit of the Positive Transcription Elongation Factor b (P-TEFb), which phosphorylates the CTD of RNAPII and negative elongation factors enabling for productive elongation after initiation. CDK9 associates with T-type cyclins and cyclin K and its activity is tightly regulated in cells at different levels. CDK9 is also the catalytic subunit of TAK (Tat activating Kinase), essential for HIV1 replication. Because of CDK9′s potential as a therapeutic target in AIDS, cancer, inflammation, and cardiomyophathy it is important to understand the consequences of CDK9 inhibition. A previous gene expression profiling study performed with human glioblastoma T98G cells in which CDK9 activity was inhibited either with a dominant negative mutant form of CDK9 (dnCDK9) or the pharmacological inhibitor Flavopiridol unveiled striking differences in gene expression effects. In the present report we extended these studies by (1) using both immortalized normal human fibroblasts and primary human astrocytes, (2) eliminating potential experimental variability due to transduction methodology and (3) also modulating CDK9 activity with siRNA.

Findings

Striking differences in the effects on gene expression resulting from the strategy used to inhibit CDK9 activity (dnCDK9 or FVP) remain even when potential variability due to viral transduction is eliminated. siRNA mediated CDK9 knockdown in human fibroblasts and astrocytes efficiently reduced CDK9 expression and led to potent changes in gene expression that exhibit little correlation with the effects of dnCDK9 or FVP. Interestingly, HEXIM1 a validated CDK9 target gene, was found to be potently downregulated by dnCDK9, FVP and siCDK9, but the cluster of genes with expression profiles similar to HEXIM1 was small. Finally, cluster analysis of all treatments revealed higher correlation between treatments than cell type origin.

Conclusion

The nature of the strategy used to inhibit CDK9 profoundly affects the patterns of gene expression resulting from CDK9 inhibition. These results suggest multiple variables that affect outcome, including kinetics of inhibition, potency, off-target effects, and selectivity issues. This is particularly important when considering CDK9 as a potential target for therapeutic intervention.

【 授权许可】

   
2014 Garriga and Graña; licensee BioMed Central Ltd.

【 图 表 】

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