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Review
. 2021 May 1;13(9):2181.
doi: 10.3390/cancers13092181.

Targeting CDK9 for Anti-Cancer Therapeutics

Ranadip Mandal  1 , Sven Becker  1 , Klaus Strebhardt  1   2
Affiliations
Review

Targeting CDK9 for Anti-Cancer Therapeutics

Ranadip Mandal et al. Cancers (Basel). .

Abstract

Cyclin Dependent Kinase 9 (CDK9) is one of the most important transcription regulatory members of the CDK family. In conjunction with its main cyclin partner-Cyclin T1, it forms the Positive Transcription Elongation Factor b (P-TEFb) whose primary function in eukaryotic cells is to mediate the positive transcription elongation of nascent mRNA strands, by phosphorylating the S2 residues of the YSPTSPS tandem repeats at the C-terminus domain (CTD) of RNA Polymerase II (RNAP II). To aid in this process, P-TEFb also simultaneously phosphorylates and inactivates a number of negative transcription regulators like 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) Sensitivity-Inducing Factor (DSIF) and Negative Elongation Factor (NELF). Significantly enhanced activity of CDK9 is observed in multiple cancer types, which is universally associated with significantly shortened Overall Survival (OS) of the patients. In these cancer types, CDK9 regulates a plethora of cellular functions including proliferation, survival, cell cycle regulation, DNA damage repair and metastasis. Due to the extremely critical role of CDK9 in cancer cells, inhibiting its functions has been the subject of intense research, resulting the development of multiple, increasingly specific small-molecule inhibitors, some of which are presently in clinical trials. The search for newer generation CDK9 inhibitors with higher specificity and lower potential toxicities and suitable combination therapies continues. In fact, the Phase I clinical trials of the latest, highly specific CDK9 inhibitor BAY1251152, against different solid tumors have shown good anti-tumor and on-target activities and pharmacokinetics, combined with manageable safety profile while the phase I and II clinical trials of another inhibitor AT-7519 have been undertaken or are undergoing. To enhance the effectiveness and target diversity and reduce potential drug-resistance, the future of CDK9 inhibition would likely involve combining CDK9 inhibitors with inhibitors like those against BRD4, SEC, MYC, MCL-1 and HSP90.

Keywords: Apoptosis; BRD4; CDK9; Cyclin T1; MYC; RNAP II; Transcription.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The PITALRE (Pro-Ile-Thr-Ala-Lue-Arg-Glu) sequence of CDK9 which aligned with the highly conserved PSTAIRE box, observed in multiple CDKs.
Figure 2
Figure 2
The domain structures of key proteins involved in P-TEFb regulated transcription. (A) The two CDK9 isoforms expressed in most cells. The CDK955 is longer than the CDK942 by 117 amino acids (aa) at the N-terminus (NT) as the former isoform is transcribed by a different promoter, <500 bp away from the later, on the CDK9 gene. The aa highlighted in blue represent the key phosphorylation sites on CDK9. The PITALRE region is marked in light black. While the three acetylation sites are highlighted in black (B) The three main cyclins that partner with CDK9. The main acetylation site E96 is highlighted in black on Cyclin T1 (C) SPT5 which is a component of the 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) Sensitivity-Inducing Factor (DSIF). It possesses upto 7 Kyrpides-Ouzounis-Woese (KOW) domains which binds to different regions of RNAP II. The RNAP II binding region of SPT5 has been highlighted in black. (D) HEXIM1. (E) LARP7 with its La-Motif (LAM) and RNA-Recognition Motifs (RRM1 and 2). The LAM and RRM1 motifs work synergistically to form a ‘V’ shaped clamp to bind to the 3′-UUUU-OH region of 7SK snRNA while the RRM2 binds to the apical loop of the 3′-hairpin of the 7SK snRNA. (F) BRD4 with its N-terminus Phosphorylation Site (NPS), two Bromodomains (BD1 and 2) and N-terminus Extra Terminal (NET) domain and the C-terminus P-TEFb Interacting Domain (PID). (G) RNAP II with its 7 Rpb1 (RNA polymerase II subunit B1) domains and the 52 Y1S2P3T4S5P6S7 heptad tandem repeats at its CTD.
Figure 3
Figure 3
The structures of key complexes involved in RNAP II mediated transcription and regulation of CDK9 activity. (A) Pre-Initiation Complex (PIC)–the PIC is composed of RNAP II which is assisted by General Transcription Factors (GTFs) like TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH. TFIID in-turn is composed of the TATA box-Binding Protein (TBP) and upto 15 TBP Associated Factors (TAF). TFIID, assisted by TFIIA, first recognizes the core promoter by scanning for and subsequently associating with the TATA box sequence on the promoter DNA. TBP then recruits the TFIIB which subsequently loads the RNAP II-TFIIF complex on the promoter. Eventually, TFIIE and TFIIH facilitates the opening of the transcription bubble [62]. (B) The TFIIH is a heterodecameric protein complex comprising of the proteins XPB, XPD, p62, p52, p44, p34 and p8 forming the core, plus CAK with CDK7, Cyclin H and MAT1. It is an essential part of PIC and is also involved in DNA repair. The DNA helicase XPD and the dsDNA translocase activity of XPB are both required for opening of the transcription bubble, although XPD is not critical for transcription initiation but for DNA damage repair. CAK (CDK7/Cyclin H) phosphorylates S5 of RNAP II, whereas MAT1 both assists in the interaction between CDK7 and Cyclin H and recruits CAK to the TFIIH core, by interacting with XPD and XPB. The function of XPB is regulated by p52 and p8 while that of XPD is regulated by p44 [46]. (C) The 7SK snRNP is composed of the non-coding 7SK snRNA, serving as as scaffold for the RNA binding proteins HEXIM1/HEXIM2, LARP7 and MePCE. (D) The Mediator Complex (MC) is comprised of upto 30 subunits in humans, which are generally divided into the head, middle, tail and kinase modules. The head is composed of the mediators 6, 8, 11, 17, 18, 20 and 22 in the head (blue); 1, 4, 7, 9, 10, 21 and 31 in the middle (black); and 15, 16, 23, 2/29, 3/27 and 5/24 in the tail (red). The mediators 31 and 14 connect the head with middle and tail with middle, respectively. The kinase domain is composed of the mediators 12 and 13, CDK8 or its paralogue CDK19 and Cyclin C. The functions of the mediators 25, 28 and 30 (*) are yet undefined. The MC promotes the assembly of the PIC by serving as a functional bridge between RNAP II and the above mentioned GTFs [63]. (E) The Super Elongation Complex (SEC) is composed of CDK9/Cyclin T1, the Eleven-nineteen Lysine-rich Leukemia (ELL) proteins 1, 2 and 3, the AF4/FMR2 Family members 1 and 4 (AFF 1 and 4), Eleven-Nineteen Leukemia (ENL), ALL1-Fused gene from chromosome 9 (AF9) and the ELL-associated factors 1 and 2 (EAF 1 and 2) [64,65].
Figure 4
Figure 4
The simplified model of the regulation of transcription by P-TEFb. (A) At the beginning of transcription, Transcription Factors (TFs) bind to the enhancer regions, upstream of the core promoter region (represented by the TATA box). The TATA box in-turn is located upstream of the Transcription Start Site (TSS). (B) TFs recruit the Mediator Complex (MC) (Simplified here from Figure 3). (C) The MC then assists in the recruitment and assembly of the PIC on the DNA strand which, as mentioned before, starts promoter melting and form the transcription bubble, to allow to the RNAP II to access the DNA template strand. (D) The TFIIH subunit of PIC also phosphorylates the S5 residue at the CTD of RNAP II to initiate transcription from the TSS to generate a nascent mRNA transcript of ~50 ribonucleotides but pauses due to recruitment of two negative regulators of transcription DSIF and NELF. The S5 phosphorylation also enables the dissociation of the MC and freeing-up of the RNAP II from the PIC and promotes the recruitment of capping enzymes to cap the 5′-end of the nascent mRNA strand in a multi-step process, to prevent the nascent strand from being degraded by nucleases like XRN2. The cap remains until transcription finishes and the mRNA is properly processed. (E) When it is ideal for the cells to carry-out productive transcription, BRD4 recruits P-TEFb (CDK9/Cyclin T1) from its negative regulatory complex—7SK snRNP to the RNAP II. However, the kinase activity of the BRD4 bound CDK9 remains transiently inhibited due to the phosphorylation of T29 of CDK9 by BRD4 (F) The phosphatase PP2α is then recruited which dephosphorylates T29, restoring the kinase activity of CDK9. This causes the additional P-TEFb mediated phosphorylations of RNAP II at S2, the SPT5 subunit of DSIF at T4 and NELF. This allows NELF to dissociate from RNAP II, which along with SPT5 phosphorylation, transforms DSIF to a positive elongation factor. These events relieve RNAP II from transcription pause and allows it to progress along with the DNA template to initiate productive transcriptional elongation. As the transcription elongation gears-up, BRD4 was released from the P-TEFb.
Figure 5
Figure 5
The alterations of the CDK9 gene in various cancer entities. The alteration frequency of the CDK9 gene in various cancers have been represented graphically. The alterations involve deletions, mutations, copy number amplifications and other alterations. The numbers on top of each cancer entity are the respective patient numbers represented. The data were obtained from www.cbioportal.org (accessed on 16 February 2021).
Figure 6
Figure 6
The alterations of the (A) BRD4 and (B) MYC genes in various cancer entities. The alteration frequency of the BRD4 and MYC genes in various cancers have been represented graphically. The alterations involve deletions, mutations, copy number amplifications, other alterations and fusions. The numbers on top of each cancer entity are the respective patient numbers represented. The data were obtained from www.cbioportal.org. (Accessed on 21 February 2021).
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References

    1. Cassandri M., Fioravanti R., Pomella S., Valente S., Rotili D., Del Baldo G., De Angelis B., Rota R., Mai A. CDK9 as a Valuable Target in Cancer: From Natural Compounds Inhibitors to Current Treatment in Pediatric Soft Tissue Sarcomas. Front. Pharmacol. 2020;11:1230. doi: 10.3389/fphar.2020.01230. - DOI - PMC - PubMed
    1. García-Reyes B., Kretz A.-L., Ruff J.-P., Von Karstedt S., Hillenbrand A., Knippschild U., Henne-Bruns D., Lemke J. The Emerging Role of Cyclin-Dependent Kinases (CDKs) in Pancreatic Ductal Adenocarcinoma. Int. J. Mol. Sci. 2018;19:3219. doi: 10.3390/ijms19103219. - DOI - PMC - PubMed
    1. Wood D.J., Endicott J.A. Structural insights into the functional diversity of the CDK–cyclin family. Open Biol. 2018;8 doi: 10.1098/rsob.180112. - DOI - PMC - PubMed
    1. Matthess Y., Raab M., Sanhaji M., Lavrik I.N., Strebhardt K. Cdk1/Cyclin B1 Controls Fas-Mediated Apoptosis by Regulating Caspase-8 Activity. Mol. Cell. Biol. 2010;30:5726–5740. doi: 10.1128/MCB.00731-10. - DOI - PMC - PubMed
    1. Matthess Y., Raab M., Knecht R., Becker S., Strebhardt K. Sequential Cdk1 and Plk1 phosphorylation of caspase-8 triggers apoptotic cell death during mitosis. Mol. Oncol. 2014;8:596–608. doi: 10.1016/j.molonc.2013.12.013. - DOI - PMC - PubMed

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