Biological Specificity of CDK4/6 Inhibitors: Dose Response Relationship, in Vivo Signaling, and Composite Response Signature
Biological Specificity of CDK4/6 Inhibitors: Dose Response Relationship, in Vivo Signaling, and Composite Response Signature
Biological Specificity of CDK4/6 Inhibitors: Dose Response Relationship, in Vivo Signaling, and Composite Response Signature
Copyright: Knudsen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY
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ABSTRACT
Recently developed potent and selective CDK4/6 inhibitors fall into two classes
based on structure and toxicity profiles in clinical studies. One class, exemplified
by palbociclib and ribociclib, exhibits neutropenia as a dose-limiting toxicity and
requires discontinuous dosing. In contrast, the structurally distinct CDK4/6 inhibitor
abemaciclib is dosed continuously, and has diarrhea and fatigue as dose-limiting
toxicities. In preclinical models, palbociclib has been extensively studied and induces
cell cycle inhibition in an RB-dependent manner. Thus far, abemaciclib has been
less extensively evaluated. We found that abemaciclib cell cycle inhibitory activity
is RB-dependent at clinically achievable concentrations. Abemaciclib elicited potent
suppression of RB/E2F regulated genes associated with prognosis in ER-positive
breast cancer. However, unlike palbociclib, at 250nM-1 µM doses abemaciclib induced
cell death in RB-deficient cell lines. This response was associated with a rapidly-
induced multi-vacuolar phenotype indicative of lysosomal membrane permeabilization
that could be ameliorated with chloroquine. This event was not a reflection of
inhibition of other CDK family members, but could be recapitulated with CBX4945 that
inhibits casein and DYRK/HIPK kinases. To determine if these “off-target” features
of abemaciclib were observed in vivo, mice harboring matched RB-positive and
negative xenografts were treated with palbociclib and abemaciclib. In vivo, all of the
apparent activity of abemaciclib was RB-dependent and strongly elicited suppression
of cell cycle regulatory genes in a fashion markedly similar to palbociclib. Using gene
expression data from cell lines and tumors treated with abemaciclib and palbociclib
a composite signature of response to CDK4/6 inhibition was developed that included
many genes that are individually required for tumor cell proliferation or viability.
These data indicate that while abemaciclib and palbociclib can exert distinct biological
and molecular effects, there are common gene expression features that could be
broadly utilized in measuring the response to CDK4/6 inhibition.
Figure 7: Composite response signature for CDK4/6 inhibitors: A. Heatmap showing genes that are consistently altered with
palbociclib (PD) and abemacicilb (LY) in RB-proficient models. RB-deficient MB468 model is shown as a control. B. Data plotting
genes within the CDK4/6 response signature that are required for viability (p < 0.05) for the indicated cell lines. The CDK4/6 response
signature genes are strongly associated with reduced viability/proliferation across all of the cell lines interrogated (two-sided test of equal
proportions, p = 4.231703e-17). Select required genes are shown for reference C. Heatmap showing the relative expression of the CDK4/6
response signature across 967 ER+ breast cancer specimens. Two major clusters are identified. D. Kaplan-Meier curve dichotomized by the
two major clusters observed in ER+ breast cancer specimens (log-rank p-value=1.378e-08).