Publication Summary

Multi-omics profiling establishes the polypharmacology of FDA Approved CDK4/6 inhibitors and the potential for differential clinical activity

Marc Hafner^*,1,3, Caitlin Elizabeth Mills^*,1, Kartik Subramanian¹, Chen Chen¹, Mirra Chung¹, Sarah A. Boswell¹, Robert A. Everley¹, Changchang Liu¹, Charlotte Sanden Walmsley², Dejan Juric^1,2,ɸ, and Peter Karl Sorger^1,†,ɸ
^*These authors contributed equally to this work.
^ɸThese authors contributed equally to this work.
¹Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115
²Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA 02114
³Current address: Department of Bioinformatics & Computational Biology, Genentech, Inc., South San Francisco, CA 94080
^† Lead contact: Peter Sorger (peter_sorger [at] hms.harvard.edu); orcid.org/0000-0002-3364-1838 copying sorger_admin [at] hms.harvard.edu).
Cell Chem Biol. 26(8):1067-1080.e8.
doi:10.1016/j.chembiol.2019.05.005 PMID:31178407 PMCID:PMC6936329

Synopsis

Figure 3e. IC₅₀ values for CDK/cyclin complexes for CDK4/6 inhibitors and alvocidib as
measured using purified kinases in vitro.

Over-expression of cyclin-dependent kinase (CDK) proteins, leading to dysregulation of the cell cycle, is common in solid tumors including breast cancer. Drugs that inhibit CDK4 and CDK6, including palbociclib (Ibrance®), ribociclib (KISQALI®) and abemaciclib (Verzenio®), are currently regarded as some of the most promising new treatments for hormone receptor-positive breast cancer. While emerging evidence suggests that these drugs differ in the clinic, their target profiles and biological activities have not been directly compared. We analyzed palbociclib, ribociclib, and abemaciclib using five complementary experimental approaches and found that they have substantial differences in biological activities and secondary targets in breast cancer cell lines. Multiple lines of evidence suggest that inhibition of additional CDK proteins by abemaciclib may be therapeutically advantageous.

Key Findings

We present six lines of evidence that alvocidib, abemaciclib, palbociclib and ribociclib span a spectrum of increasing selectivity for CDK4/6-cyclin complexes.

Abemaciclib has biochemical and physiological activities, including CDK1 and CDK2 inhibition, not manifested by ribociclib and only weakly by palbociclib.

The substantially wider spectrum of activities detected for abemaciclib relative to other CDK4/6 inhibitors provides a rationale for treating patients with abemaciclib following disease progression on palbociclib or ribociclib.

While drug development efforts have focused on increasing selectivity as a means of reducing toxicity, off-target activity can be exploited to achieve a more durable response.

Abstract

The target profiles of many drugs are established early in their development and are not systematically revisited at the time of FDA approval. Thus, it is often unclear whether therapeutics with the same nominal targets but different chemical structures are functionally equivalent. In this paper we use five different phenotypic and biochemical assays to compare approved inhibitors of cyclin-dependent kinases 4/6 – collectively regarded as breakthroughs in the treatment of hormone receptor-positive breast cancer. We find that transcriptional, proteomic and phenotypic changes induced by palbociclib, ribociclib, and abemaciclib differ significantly; abemaciclib in particular has advantageous activities partially overlapping those of alvocidib, an older polyselective CDK inhibitor. In cells and mice, abemaciclib inhibits kinases other than CDK4/6 including CDK2/Cyclin A/E ¬– implicated in resistance to CDK4/6 inhibition – and CDK1/Cyclin B. The multi-faceted experimental and computational approaches described here therefore uncover under-appreciated differences in CDK4/6 inhibitor activities with potential importance in treating human patients.

Datasets and Associated Metadata and Code

The following data are available for download.

Table	Description	HMS LINCS ID	Synapse ID	Other Resources
S1	DGE-seq Gene expression data for 7 cell lines treated with abemaciclib, palbociclib, ribociclib at 0.1, 0.3, 1, or 3 μM, or alvocidib at 0.1 or 1 μM for 6 hours.		syn18488088	GEO GSE125215
S1	Enrichment analysis of genes in signature 1 (CDK4/6 inhibitor signature) and signature 2 (abemaciclib-specific signature).		syn18488087
S1	mRNA-seq gene expression data for seven cell lines treated with one of three CDK4/6 inhibitors at 0.3, 1.0, or 3.0 μM for 6 or 24 hours.		syn18488086	GEO GSE99116
S1	mRNA-seq gene expression data for MCF7 xenografts treated with ribociclib, palbociclib, abemaciclib or vehicle.		syn18488096	GEO GSE124854
S2	Kinase set library.		syn18508419
S2	Inferred differential kinase activity for MCF7 cells treated with palbociclib or abemaciclib at either 0.3 or 3.0 μM.		syn18488090
S2	Differentially expressed phosphopeptides in MCF7 cells treated with palbociclib or abemaciclib at either 0.3 or 3.0 μM and untreated controls.		syn18488089
S3	KINOMEscan results for ribociclib, palbociclib, or abemaciclib at 0.1 and 1.0 μM.	20330, 20339, 20338	syn18488091
S4	Differentially inhibited kinases in lysates treated with ribociclib, palbociclib or abemaciclib at 0.1, 1, or 10 μM and untreated controls measured by MIB/MS.		syn18488092
S5	IC50 values for inhibition or binding of kinases by ribociclib, palbociclib, abemaciclib, and alvocidib.		syn18488093
S6	GR metrics and biphasic fitting parameters for the response of 34 breast cancer cell lines to palbociclib and abemaciclib.	20344	syn18488095
S6	GR values and increased fraction of dead cells for the response of MCF7 and Hs 578T parental and 1μM-palbociclib adapted cells to ribociclib, palbociclib, and abemaciclib.		syn18488098
S6	GR values and increased fraction of dead cells for the response of patient-derived MGH312 cells to ribociclib, palbociclib, and abemaciclib.		syn18488099
S6	GR values and increased fraction of dead cells for the response of 34 breast cancer cell lines to palbociclib and abemaciclib.	20343	syn18488094
S6	Time-dependent GR values and increased fraction of dead cells for the response of MCF7, Hs 578T, and PDX12-58 cells to ribociclib, palbociclib, and abemaciclib.		syn18488097

Funding Sources