Chordoma Foundation


Cyclin-dependent kinase 4 (CDK4) and Cyclin-dependent kinase 6 (CDK6) are serine-threonine kinases that regulate cell cycle progression through the G1 phase. CDK4/6 are activated by D-type cyclins to progress cells past the G1/S phase checkpoint in the cell cycle. The primary role of CDK4/6 is to phosphorylate and inactivate the RB tumor suppressor, leading to induction of genes related to cell proliferation. CDKN2A (p16) inhibits CDK4/6 kinase activity.1

Location: CDK4 chromosome 12q14.4; CDK6 chromosome 7q21.2

CDK4 and CDK6 are oncoproteins that are normally controlled by the CDKN2A gene (p16 protein). Upregulation of CDK4/6 or inactivation of CDKN2A can lead to cell cycle deregulation, increased cell proliferation, and tumorigenesis.

CDK4/6 in Chordoma

  • CDK4 and CDK6 (CDK4/6) are frequently aberrantly activated in chordoma due to loss of a natural CDK4/6 inhibitor called p16, which is encoded by the CDKN2A gene. CDKN2A is a bona fide tumor suppressor gene because p16 is a critical regulator of CDK4/6-mediated cell growth and proliferation.  Several other potential therapeutic targets in chordoma are thought to exert their oncogenic effects, at least in part, by activating CDK4/6.  Indeed, loss of CDKN2A has been associated with aggressive behavior in other cancers2. Pharmaceutical inhibitors of CDK4/6, several of which are already FDA-approved in other cancer types, can neutralize the consequences of CDKN2A/p16 loss and potentially improve patient outcomes.
  • Molecular Evidence
  • Preclinical Evidence
  • Open Clinical Trials

Molecular Evidence

Gene Expression

  • CDK4 and CDK6 mRNA was expressed in 8/8 cell lines tested: U-CH1, U-CH2, U-CH3, U-CH6, U-CH7, U-CH10, U-CH11, U-CH12.3

Gene Mutation

  • Somatic alterations believed to be targeted by CDK4/6 inhibitors have been observed in patient tumors, including amplification of CDK4 and mutations in PIP4K2A.4

Protein Expression

  • CDK4 and CDK6 protein has been detected in 8/8 cell lines tested: U-CH1, U-CH2, U-CH3, U-CH6, U-CH7, U-CH10, U-CH11, U-CH12.3 CDK4 protein has also been detected in Mug-Chor1 and CH22; CDK6 protein was detected in Mug-Chor1 but absent in CH22.5
  • CDK4 was overexpressed in 5/25 (20%) of patient cases as measured by immunohistochemistry. Overexpression of CDK4 was associated with increased proliferation (high MIB labeling index), positive p53 expression, and the presence of mitotic figures.6
  • 7/10 freshly isolated primary chordoma cases had high expression of CDK4, 1/10 had intermediate expression of CDK4 and 2/10 had low expression of CDK4 as measured by western blot. All cases were negative for p16 protein expression. Most of the cases that expressed CDK4 also expressed CDK6, Rb, and pRb.5
  • CDK4 expression levels as measured by tissue microarray (TMA) immunohistochemical staining of 85 samples from 72 chordoma patients found that 97.7% of the chordoma tissue samples expressed CDK4 and 50.6% of the samples were classified as staining highly for CDK4. The mean CDK4 expression score in specimens from metastatic disease or recurrent status was significantly higher than those from primary specimens and the mean expression level of CDK4 for non-survivors was significantly higher than the survivors. There was no correlation between CDK4 expression and age at surgery, gender, or tumor location.5

Preclinical Evidence

In-vitro Efficacy

  • Palbociclib: Treatment of chordoma cells with the CDK4/6 inhibitor palbociclib resulted in decreased cell growth and decreased pRb (S780) expression corresponding to increased concentrations of palbociclib. This finding was true for all 8 chordoma cell lines tested (U-CH1, U-CH2, U-CH3, U-CH6, U-CH7, U-CH10, U-CH11, U-CH12) although there was some variation between cell lines.3 5
  • Palbociclib: For the analyzed cell lines U-CH2, U-CH3, U-CH6 and U-CH7, the IC50 value for palbociclib was between 50 and 100 nmol/L and U-CH11 had a higher IC50 of 300-400 nmol/L.3
  • Palbociclib: Treatment of U-CH1 and U-CH2 with palbociclib showed an increase of cells in G1 phase and decrease in S and G2. Additionally, cleaved PARP and cleaved caspase-3 were not detected, suggesting that palbociclib works by inhibiting cell proliferation and does not induce apoptosis.3
  • LY2835219 (abemaciclib): Treatment of U-CH1 and U-CH2 with the CDK4/6 inhibitor LY2835219 inhibited cell viability.3
  • Palbociclib: U-CH2 and CH22 cell lines treated with palbociclib had IC50 values at 0.1575 and 0.3929 mM, respectively, and cell count was found to decrease in relation to increasing concentrations of palbociclib. Treatment with pablociclib was found to decrease pRb protein levels without affecting Rb, CDK4 or CDK6 protein expression. Cell cycle analysis revealed that CDK4-inhibition induced cell cycle arrest in G1 phase and inhibition of DNA synthesis.5
  • CDK4 siRNA knockdown: Knockdown of CDK4 via siRNA transfection in U-CH2 and CH22 cell lines resulted in repression of cell migration, dose-dependent inhibition of cell proliferation, and inhibition of CDK4 expression and reduction of pRb expression without alteration of CDK6 or Rb expression.5

In-vivo Efficacy

  • The following drugs have been tested in patient and cell-derived xenograft models as part of the Chordoma Foundation’s Drug Screening Program. Information on the specific PDX and CDX models used for drug testing can be found here and figures are available on the digital data repository, Figshare.
    • Palbociclib: Significant tumor growth inhibition was observed in 5/6 xenograft models tested and provided scientific rationale for a chordoma-specific clinical trial
    • Palbociclib + Cetuximab: A synergistic effect and significant tumor growth inhibition was observed in the SF8894 chordoma xenograft model
    • Ribociclib: Significant tumor growth inhibition was not observed in the SF8894 chordoma xenograft model

Open Clinical Trials

The following clinical trials have been launched to explore whether targeting CDK4/6 is effective in treating chordoma patients. Visit our Clinical Trials page to view a list of other clinical trials available to chordoma patients and to find out who to contact if you wish to participate.

Trial Identifier



NCT03110744 CDK4/6 Inhibition in Locally Advanced/Metastatic Chordoma National Center for Tumor Diseases (Heidelberg, Germany)

Sherr C, Beach D, Shapiro G. Targeting CDK4 and CDK6: From Discovery to Therapy. Cancer Discov. 2016;6(4):353-367. [PubMed]
Horbinski C, Oakley G, Cieply K, et al. The prognostic value of Ki-67, p53, epidermal growth factor receptor, 1p36, 9p21, 10q23, and 17p13 in skull base chordomas. Arch Pathol Lab Med. 2010;134(8):1170-1176. [PubMed]
von W, Goerttler L, Marienfeld R, et al. Preclinical Characterization of Novel Chordoma Cell Systems and Their Targeting by Pharmocological Inhibitors of the CDK4/6 Cell-Cycle Pathway. Cancer Res. 2015;75(18):3823-3831. [PubMed]
Liang W, Dardis C, Helland A, et al. Identification of therapeutic targets in chordoma through comprehensive genomic and transcriptomic analyses. Cold Spring Harb Mol Case Stud. Published online October 15, 2018. [PubMed]
Liu T, Shen J, Choy E, et al. CDK4 expression in chordoma: A potential therapeutic target. J Orthop Res. Published online November 30, 2017. [PubMed]
Yakkioui Y, Temel Y, Creytens D, et al. A comparison of cell-cycle markers in skull base and sacral chordomas. World Neurosurg. 2014;82(1-2):e311-8. [PubMed]

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