CDK9 inhibition blocks the initiation of PINK1-PRKN-mediated mitophagy by regulating the SIRT1-FOXO3-BNIP3 axis and enhances the therapeutic effects involving mitochondrial dysfunction in hepatocellular carcinoma

Mitophagy, a selective form of macroautophagy, is responsible for degrading damaged or excess mitochondria, playing a crucial role in maintaining cellular homeostasis and contributing to acquired drug resistance. Despite its importance, the regulatory mechanisms of mitophagy in cancer remain unclear. In this study, we found that inhibiting CDK9 disrupts PINK1-PRKN-mediated mitophagy in hepatocellular carcinoma (HCC) by blocking the initiation of this process. Our research showed that CDK9 inhibitors induce the dephosphorylation of SIRT1 and promote the degradation of FOXO3, which is regulated by its acetylation. This leads to the transcriptional suppression of FOXO3-driven BNIP3 and destabilizes PINK1 protein, thereby impairing mitophagy. Notably, lysosomal degradation inhibitors could not restore the mitophagy flux blocked by CDK9 inhibitors. Thus, CDK9 inhibitors effectively inactivate the SIRT1-FOXO3-BNIP3 axis and the PINK1-PRKN pathway, thereby halting the initiation of mitophagy. Additionally, CDK9 inhibition leads to mitochondrial dysfunction, causing a loss of mitochondrial homeostasis and cell death in HCC.

A novel CDK9 inhibitor, oroxylin A (OA), derived from Scutellaria baicalensis, demonstrated significant therapeutic potential against HCC and was particularly effective in overcoming drug resistance by downregulating PINK1-PRKN-mediated mitophagy. Importantly, OA’s moderate inhibition of CDK9 did not result in excessive repression of general transcription, avoiding the inconsistent anti-HCC efficacy and high toxicity associated with existing CDK9 inhibitors. These findings suggest that disrupting mitophagy is a Aloxistatin promising strategy for treating HCC, and OA represents a potential candidate for developing mitophagy inhibitors.