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Transcription-Associated Cyclin-Dependent Kinases As Targets and Biomarkers for Cancer Therapy

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Transcription-Associated Cyclin-Dependent Kinases As Targets and Biomarkers for Cancer Therapy Published OnlineFirst February 18, 2020; DOI: 10.1158/2159-8290.CD-19-0528 REVIEW Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy Jonathan Chou1,2, David A. Quigley1,3, Troy M. Robinson1,4, Felix Y. Feng1,2,4,5, and Alan Ashworth1,2 ABSTRACT Drugs targeting the cell cycle–regulatory cyclin-dependent kinase (CDK) 4 and 6 have been approved for the treatment of hormone receptor–positive breast cancer, and inhibitors targeting other cell-cycle CDKs are currently in clinical trials. Another class of CDKs, the transcription-associated CDKs, including CDK7, CDK8, CDK9, CDK12 and CDK13, are critical regula- tors of gene expression. Recent evidence suggests several novel functions of these CDKs, including regulation of epigenetic modifications, intronic polyadenylation, DNA-damage responses, and genomic stability. Here, we summarize our current understanding of the transcriptional CDKs, their utility as biomarkers, and their potential as therapeutic targets. Significance: CDK inhibitors targeting CDK4 and CDK6 have been approved in hormone receptor–posi- tive breast cancer, and inhibitors targeting other cell-cycle CDKs are currently in clinical trials. Several studies now point to potential therapeutic opportunities by inhibiting the transcription-associated CDKs as well as therapeutic vulnerabilities with PARP inhibitors and immunotherapy in tumors deficient in these CDKs. INTRODUCTION subunit (RPB1) of RNA polymerase II (RNA Pol II), as well as other targets. However, their precise mechanisms of action The cyclin-dependent kinases (CDK) are a family of approx- related to transcription remain relatively obscure (1). In addi- imately 20 serine/threonine kinases that regulate fundamen- tion, there remains a class of CDKs for which the underlying tal cellular processes. They are broadly divided into two major functions are largely unknown. Each of the CDKs is bound to subclasses: (i) cell cycle–associated CDKs (including CDK1, a specific cyclin, which directs the activity of the CDK. Given CDK2, CDK4, and CDK6) that directly regulate progression that CDKs control processes critical for cancer cell survival through the phases of the cell cycle and (ii) transcription- and growth, they have been viewed as promising therapeutic associated CDKs (including CDK7, CDK8, CDK9, CDK12, targets. Indeed, multiple CDK inhibitors have been developed and CDK13). The transcription-associated CDKs regulate and tested in a number of cancer types (reviewed in ref. 1). gene transcription by phosphorylating the carboxy-termi- Recently, inhibitors that target CDK4/CDK6 (e.g., palboci- nal domain (CTD) of the DNA-directed RNA polymerase II clib, ribociclib, and abemaciclib) have become widely used in hormone receptor–positive [i.e., estrogen receptor (ER) and/ 1Helen Diller Family Comprehensive Cancer Center, University of California, or progesterone receptor–expressing] breast cancer, and have San Francisco, San Francisco, California. 2Department of Medicine, Divi- shown impressive improvements in progression-free survival sion of Hematology/Oncology, University of California, San Francisco, (PFS) and overall survival (OS; refs. 2–4). Moreover, inhibitors San Francisco, California. 3Department of Epidemiology and Biostatistics, that target CDK1 and CDK2 are currently in clinical trials for 4 University of California, San Francisco, San Francisco, California. Depart- multiple cancer types (5). ment of Radiation Oncology, University of California, San Francisco, San Francisco, California. 5Department of Urology, University of California, In contrast, the transcription-associated CDKs are less San Francisco, San Francisco, California. developed as therapeutic targets, and small-molecule inhibi- Note: Supplementary data for this article are available at Cancer Discovery tors of transcription-associated CDKs have not yet entered Online (http://cancerdiscovery.aacrjournals.org/). routine clinical use. However, several recent studies implicate Corresponding Author: Alan Ashworth, UCSF Helen Diller Family Com- these CDKs in driving and maintaining cancer cell growth, prehensive Cancer Center, 1450 3rd Street, Box 0128, San Francisco, particularly in cancers primarily driven by dysregulated tran- CA 94158-0128. Phone: 415-476-5876; E-mail: [email protected] scription factors, such as those dependent on MYC (e.g., Cancer Discov 2020;10:1–20 neuroblastoma) or the EWS–FLI1 fusion oncoprotein (Ewing doi: 10.1158/2159-8290.CD-19-0528 sarcoma). Mounting evidence suggests that inhibiting this ©2020 American Association for Cancer Research. class of CDKs may have important therapeutic relevance. march 2020 CANCER DISCOVERY | OF1 Downloaded from cancerdiscovery.aacrjournals.org on September 28, 2021. © 2020 American Association for Cancer Research. Published OnlineFirst February 18, 2020; DOI: 10.1158/2159-8290.CD-19-0528 REVIEW Chou et al. In addition, some transcription-associated CDKs, such as can also associate with the Mediator complex to regulate CDK12, are inactivated in ovarian and prostate cancers, sup- transcription in a gene-specific manner (25) and has kinase- porting a tumor-suppressive role for these transcriptional independent roles in regulating the p53 stress response (28). CDKs. Here, we review our current understanding of the A large-scale proteomics study recently identified more than transcription-associated CDKs and highlight the genomic 60 proteins phosphorylated by CDK8 and CDK19, many features of tumors carrying transcriptional CDK loss-of-func- of which are associated with chromatin modification, DNA tion mutations and potential synthetic lethal approaches. We repair, and transcription (29). discuss the utility of using transcription-associated CDKs CDK12 was discovered as a CDC2-related kinase with an as biomarkers for targeted therapies, potential combination arginine/serine rich (RS) domain (also known as CRKRS; ref. strategies with checkpoint immunotherapy, and the recent 30). The CRKRS/CDK12 gene encodes a protein of 1,490 amino development of small-molecule inhibitors against transcrip- acids and is one of the largest CDKs, encompassing a carboxy- tional CDKs in various cancer types. terminal kinase domain, two proline-rich motifs (PRM) involved in protein–protein interactions, and an RS domain that is com- monly found in splicing factors of the serine/ arginine-rich STRUCTURE AND FUNCTION OF family (ref. 30; Fig. 1A). Within the nucleus, CDK12 localizes in TRANSCRIPTION-ASSOCIATED CDKs a speckled pattern, overlapping with spliceosome components Each of the transcription-associated CDKs binds to an (30). CDK12 is essential during embryonic development, and activating cyclin partner to regulate gene transcription (6). knockout of the gene in mouse embryonic stem (ES) cells leads CDK7 (also known as CDKN7) is a 346 amino acid protein to lethality shortly after implantation; Cdk12−/− blastocysts fail (Fig. 1A) that binds to cyclin H and the accessory protein to undergo outgrowth of the inner cell mass due to apoptosis MAT1 to function as a CDK-activating kinase (CAK), and and exhibit increased spontaneous DNA damage (31). The has a general role in transcription: by phosphorylating search for cyclin partners initially identified cyclins L1 and L2 as the CTD of RNA Pol II, CDK7 regulates the initiation of cognate cyclins for CDK12 (32), but cyclin K was later shown to transcription and promoter escape (7, 8). The CDK7/CAK be the bona fide CDK12-associating cyclin critical for its kinase complex, which associates with the core TFIIH complex, activity (33–35). can activate CDK9 (PITALRE, CDC2L4, CTK1) by phos- The closest related CDK to CDK12 is CDK13 (also known phorylating the threonine-186 residue within the activating as CDC2L5, CHED), which is also a large CDK consisting T-loop. This cascade of events controls the switch from tran- of 1,512 amino acids. CDK12 and CDK13 share 50% amino scriptional initiation to elongation of RNA Pol II (9). Several acid identity overall, having unrelated amino and carboxy- recent reviews on have been published on the functions of terminal domains. CDK13 contains a carboxy-terminal ser- CDK7 (10, 11). ine-rich (SR) domain and two alanine-rich (AR) domains, CDK9, a 372 amino acid protein, binds to either cyclin T which are not found in CDK12 (ref. 36; Fig. 1A). However, or cyclin K for its kinase activity (12, 13). The CDK9 com- the kinase domains of CDK12 and CDK13 are nearly 92% plex with cyclin T, referred to as the positive transcription identical. elongation factor b (P-TEFb), is a general transcription fac- Structural studies of CDK12 and CDK13 have demon- tor (GTF) that is required for efficient expression of most strated that the amino-terminal lobe of the CDK12 kinase genes and phosphorylates the CTD of RNA Pol II, as well domain interfaces with the cyclin box of cyclin K, creating as the DRB sensitivity–inducing factor (DSIF) and negative CDK12:cyclin K heterodimers, which then further dimer- elongation factor (NELF), to relieve promoter pausing and ize (35). Similar heterodimers between CDK13 and cyclin K promote transcription elongation (14). CDK9 preferentially have also been observed (37). However, despite the similari- localizes to the nonnucleolar nucleoplasm with significant ties between CDK12 and CDK13, each seems to regulate the enrichment at nuclear speckles and is thought to also func- expression of a distinct set of genes (37, 38). These data sug- tion in RNA processing and replication stress responses (15, gest shared but nonoverlapping
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