P16 methylation increases the sensitivity of cancer cells to the CDK4/6 inhibitor palbociclib

Abstract

The P16 (CDKN2Aink4a) gene is an endogenous CDK4/6 inhibitor. Palbociclib (PD0332991) is an anti-CDK4/6 chemical for cancer treatment. P16 is most frequently inactivated by copy number deletion and DNA methylation in cancers. It is well known that cancer cells with P16 deletion are more sensitive to palbociclib than those without. However, whether P16 methylation is related to palbociclib sensitivity is not known. By analyzing public pharmacogenomic datasets, we found that the IC50 of palbociclib in cancer cell lines (n = 522) was positively correlated with both the P16 expression level and P16 gene copy number. Our experimental results further showed that cancer cell lines with P16 methylation were more sensitive to palbociclib than those without. To determine whether P16 methylation directly increased the sensitivity of cancer cells to palbociclib, we induced P16 methylation in the lung cancer cell lines H661 and HCC827 and the gastric cancer cell line BGC823 via an engineered P16-specific DNA methyltransferase (P16-Dnmt) and found that the sensitivity of these cells to palbociclib was significantly increased. The survival rate of P16-Dnmt cells was significantly lower than that of vector control cells 48 hrs post treatment with palbociclib (10 μM). Notably, palbociclib treatment also selectively inhibited the proliferation of the P16-methylated subpopulation of P16-Dnmt cells, further indicating that P16 methylation can increase the sensitivity of cells to this CDK4/6 inhibitor. These results were confirmed in an animal experiment. In conclusion, inactivation of the P16 gene by DNA methylation can increase the sensitivity of cancer cells to palbociclib.

High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer

“…Similarly, in the phase I trial of abemaciclib the best BC responder harbored a concomitant deletion of CDKN2A and CDKN2B in her tumor 43 . This observation is in line with the limited capacity of current CDK4/6i to inhibit its target when it is bound to p16 31,44 and consistent with the increased sensitivity to palbociclib observed in 544 cancer cell lines in association with CDKN2A inactivation by DNA methylation 45 .…”

Methylation and Noncoding RNAs in Gastric Cancer: Everything Is Connected

“…The detection of promoter hypermethylation as an epigenetic marker may be an efficient method for tumor diagnostics. For example, the promoter of p16 ( INK4a ) is hypermethylated in GC; therefore, p16 methylation could be a candidate biomarker for detection of gastric cancer [ 107 ]. Methylated ncRNAs of different classes are also applicable to GC diagnostics [ 62 ].…”

Sex and Race-Related DNA Methylation Changes in Hepatocellular Carcinoma

“…Palbociclib and Ribociclib are two FDA-approved CDK4/6 inhibitors for cancer treatment. One study showed that p16 INK4A methylation increased tumor sensitivity to the CDK4/6 inhibitor Palbociclib [52], suggesting that this might be an example of oncogene addiction. If sexbased differences in p16 INK4A promoter methylation are validated, this may be an avenue for sex-selective therapeutic protocols.…”