Cyclin-Dependent Kinase 11 (CDK11) is a serine/threonine kinase encoded at human locus 1p36.3 by two paralogous genes CDK11A and CDK11B. CDK11 has diverse roles in the regulation of transcription, splicing, apoptosis and mitosis. In proliferating cells, two predominant isoforms are expressed: CDK11p58 and CDK11p110. CDK11p110 is expressed throughout the cell cycle and regulates transcription and splicing. CDK11p58 is expressed at mitosis via IRES-dependent translation; it mediates mitotic progression and faithful chromosome segregation. Loss of Cdk11 in murine models causes early embryonic lethality, demonstrating that CDK11 is essential for normal development. Furthermore, dysregulated CDK11 expression is associated with numerous late-onset disease states, indicating its importance in adult life. In cancer, abnormal expression of CDK11 correlates with poor prognosis in a variety of tumours. Moreover, deletion of the chromosomal region 1p36.3, containing the CDK11 locus, is frequently observed in cancer and has recently been identified in a case of the development disorder, Cornelia de Lange Syndrome (CdLS). This thesis aimed to examine the functions of CDK11 and the impact of their dysregulation in cancer and developmental phenotypes. The initial aim was to investigate the novel role for CDK11 in regulating autophagy in cancer cells; CDK11 depletion causes a marked autophagy phenotype, with accumulation of autophagy protein LC3. I demonstrate that this CDK11-mediated autophagy occurs as a consequence of mitotic dysregulation. Subsequently, I examined the role of autophagy following aberrant mitosis and chromosome missegregation. I show that autophagy is important in the maintenance of aneuploid karyotypes, with loss of autophagy impairing the survival of aneuploid cell populations. I then investigated the effects of CDK11 in regulating cancer cell motility and determined that CDK11 depletion retards cancer cell migration. However, I was unable to identify any failure in cell adhesion or cell polarization to explain this migration phenotype. Subsequently, I interrogated the CDK11 interactome to further characterize the mechanisms through which CDK11 regulates both novel and established functions. This work indicated the involvement of the distinct CDK11 isoforms in pathways that have not previously been reported. This included the interaction of CDK11p110 with ribosomal and spliceosomal proteins during mitosis and the interaction of CDK11p58 with spliceosomal and proteosomal constituents also during mitosis. These findings may provide the foundation for further study. Finally I describe work undertaken to sequence the CDK11 locus in a cohort of CdLS patients, with no known causative genetic mutation, to investigate CDK11A/CDK11B as candidate disease-associated genes. Although no causative mutation in CDK11A or CDK11B was identifying, sequencing of this region indicated NCBI and UCSC genome assemblies of this locus were inaccurate due to the genomic duplication. This has been confirmed by others and corrected in the most recent genome assemblies.

The budding yeast cell cycle has attracted attention from many experimentalists over the years for its simplicity and amenability to genetic manipulation. Moreover, the regulatory components described in budding yeast, Saccharomyces cerevisiae, are conserved in higher eukaryotes. The budding yeast cell cycle is governed by a complex network of chemical reactions controlling the activity of the cyclin-dependent kinases (CDKs), proteins that drive the major events of the cell cycle. The presence of these proteins is required for the transition from G1 to S phase (Start) whereas their absence permits the transition from S/M to G1 phase (Finish). The cell cycle of budding yeast is based on alternation between these two states. To test the accuracy of this theory against experiments, we built a hypothetical molecular mechanism of the budding yeast cell cycle and transcribed it into differential equations. With a proper choice of kinetic parameters, the differential equations reproduce the main events of the cell cycle such as: the synthesis of cyclins (Cln1,2; Cln3; Clb1,2; Clb5,6) by their transcription factors (SBF, Mcm1, MBF); their association with stoichiometric inhibitors (Sic1, Cdc6); their degradation by SCF and adaptors of the APC (Cdc20, Cdh1). The emphasis was put on mechanisms responsible for the release of Cdc14 from the RENT complex, Cdc14 being a major player in exit from mitosis. Simulations of the wild type strain and more than 100 mutants showed phenotypes in accordance with experimental observations. Some mutants defective in the Start and Finish transitions and the different ways to rescue them will be presented. / Ph. D.

When unreplicated or damaged DNA is present, cell cycle checkpoint pathways cause cell cycle arrest by inhibiting cyclin-dependent kinases (Cdks). In Xenopus laevis, early embryonic development consists of twelve rapid cleavage cycles between DNA replication (S) and mitosis (M) without checkpoints or gap phases. However, checkpoints are engaged in Xenopus once the embryo reaches the midblastula transition (MBT). At this point, the embryo initiates transcription, acquires gap phases between S and M phases, and establishes a functional apoptotic program. During the cell cycle, there are two main checkpoints that regulate entrance into S and M phases. The focus of this study is the role of protein kinase Chk1 and the phosphatase Cdc25A in the DNA replication checkpoint. In the absence of active Chk1, Cdc25A activates cyclin dependent kinases (Cdks) allowing the cell to progress into S or M phase. Chk1 regulates cell cycle arrest in the presence of unreplicated DNA in somatic cells by phosphorylating Cdc25A and leading to its degradation. Chk1 is also transiently activated at the MBT in Xenopus laevis embryos, even when there is no block to DNA replication or damaged DNA. One goal of this work is to understand the developmental role and regulation of checkpoint signaling pathways due to its monitoring of DNA integrity within the cell. Chk1 plays a critical but not fully understood role in cell cycle remodeling and early embryonic development. In order to understand the function and regulation of Chk1 in checkpoints, the features of the MBT that activate Chk1 must be identified. The activation of Chk1 by two time-dependent events in the cell cycle, the critical nuclear to cytoplasmic (N/C) ratio and the cyclin E/Cdk2 maternal timer are explored in this study. Embryos treated with aphidicolin, resulting in a halted replication fork and therefore a reduced DNA concentration, were tested for Chk1 activation and Cdc25A degradation. Chk1 and Cdc25A were observed to undergo activation and degradation, respectively, in embryos with a reduced DNA concentration. In addition, embryos were injected with Δ34Xic cyclin E/Cdk2 inhibitor, in order to disturb the maternal timer and tested for Chk1 activation and Cdc25A degradation. Both Chk1 and Cdc25A were unaffected by the disruption of the cyclin E/Cdk2 maternal time in the embryo. Therefore, the N/C ratio and the cyclin E/Cdk2 maternal timer do not affect Chk1 activation and therefore Cdc25A degradation. Another means of characterizing the unreplicated DNA checkpoint is through the use of mathematical modeling of the checkpoint-signaling cascade of the cell cycle. Mathematical modeling is the translating of biological pathways into mathematical equations that can simulate interactions without performing laboratory experiments. The Novák-Tyson checkpoint model made important predictions of hysteresis and bistability in the frog egg checkpoint model, predictions that were later confirmed experimentally. The model was updated with additional interactions, such as those including Myt1, a second inhibitor kinase, and lamin proteins, which become phosphorylated at the onset of nuclear envelope breakdown (NEB) at entry into mitosis. Also, experimental data was fit into the model while maintaining hysteresis and bistability. Therefore, the unreplicated DNA checkpoint model was updated with new interactions and experimental data while still preserving previously identified dynamic characteristics of the system. As described, Cdc25A regulation is dynamic in the embryo. The checkpoint original model represents the activity of Cdc25 phosphatase on the mitosis promoting factor (MPF) that leads the cell into mitosis. In the checkpoint model, Cdc25C is the phosphatase activating MPF. However, the model does not include Cdc25A, which is an integral part of the checkpoint-signaling pathway due to its role in activating the cyclin/Cdk complex allowing entry into S and possibly M phase. Experimental studies were performed in which Cdc25A levels were reduced in embryos and extracts using Cdc25A morpholinos. Embryos and extracts showed delayed cell cycle and mitotic entry, demonstrating the importance of Cdc25A plays in the cell cycle. Based upon experimental data, the mathematical model of the DNA replication checkpoint was expanded to include Cdc25A. The expanded model should more accurately demonstrate how checkpoints affect the core cell cycle machinery. Cdc25A was incorporated into the model by gathering experimental data and designing a signaling cascade, which was translated into differential equations. The updated model was then used to simulate the effect of synthesis and degradation rates of Cdc25A on the entry into mitosis dynamics. Therefore, using mathematical modeling and experimental design, we can further understand the role that Cdc25A plays in cell cycle progression during development. Understanding the regulation of Chk1 activity at the MBT and the role of Cdc25A in checkpoint signaling will help us further characterize the dynamics of early embryonic development. The use of mathematical modeling and experimental tools both contribute to further our understanding of controls of the checkpoint signaling pathway and therefore leading us one step closer to truly being able to model a pathway and make predictions as to the behavior of the cell during early embryonic development. / Ph. D.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Correct regulation of transcription is essential for maintaining a healthy cellular state. During transcription RNA polymerase II (Pol II) proceeds in a regulated manner through several transitions to ensure appropriate control of synthesis and enable correct processing of the pre-RNA. Shortly after initiation Pol II is caused to pause by the binding of factors, DSIF and NELF. To enable transition of Pol II into the elongation phase CDK9/cyclin T phosphorylates the C-terminal domain (CTD) of Pol II, DSIF and NELF. This phosphorylation releases the paused state and provides an alternative set of post-transcriptional modifications on the CTD to generate a binding platform for elongation, histone modifying and termination factors. CDK9/cyclin T is itself regulated within multicomponent complexes. A small activated complex, containing Brd4, recruits CDK9/cyclin T to active sites of transcription, thereby promoting the elongation of transcription. The role of CDK9/cyclin T in the regulation of transcription has resulted in its validation as a drug target against several disease states including cancer, HIV and cardiac hypertrophy. In this thesis, I present the crystallographic structures of a series of 2-amino-4-heteroaryl-pyrimidine compounds and the roscovitine derivative, (S)-CR8, bound to CDK9/cyclin T and CDK2/cyclin A. In combination with thermal denaturation data and kinetic analysis, these structures have suggested chemical modifications that might be made to increase the CDK9 specificity of these compounds. I have also validated the use of a mutated form of cyclin T for use in the development of CDK9/cyclin T inhibitors. In addition, I present both structural and kinetic analysis of the Brd4-CDK9/cyclin T interaction. I show that C-terminal fragments of Brd4 enhance the in vitro kinase activity of CDK9/cyclin T against the Pol II CTD. Furthermore, I demonstrate that this enhancement may be inhibited by Plk1-mediated phosphorylation of Brd4. Finally, I show that Brd4 binds to a site that spans CDK9 and cyclin T and I propose detailed molecular models of the Brd4-cyclin T interaction.

Cardiac hypertrophy leading to heart failure remains a leading cause of morbidity and mortality in the 21st century despite major therapeutic advances. Improved understanding of novel molecular and cellular processes contributing to cardiac hypertrophy therefore continues to be important. Cyclin-dependent Kinase 9 (CDK9), part of a family of proteins controlling cell cycle and growth, has emerged as one such potential candidate over the last 5 years. CDK9 is the catalytic subunit of the CDK9/CyclinT complex and acts by phosphorylating the carboxy-terminal domain of RNA polymerase II. Hypertrophic signals, such as Endothelin-1 (ET-1) and phenylephrine, have been shown to cause CDK9 activation leading to a hypertrophic response in cultured mouse cardiomyocytes associated with reactivation of the foetal gene program. CDK9 also forms a complex with GATA4 to play a role in differentiation of mouse ES cells into cardiomyocytes. These findings suggest a specific role for CDK9 in controlling growth and differentiation of cardiomyocytes and merits further study in models where cardiomyocyte differentiation and proliferation are key contributors. In contrast to mammals, zebrafish retain a high cardiomyocyte proliferative capacity throughout their life span and can readily repair following injury. I have examined the role of CDK9 on global and cardiac development in the zebrafish embryo. I have also assessed the impact of CDK9 manipulation on response to ventricle injury using a laser-induced injury model developed and validated as part of my thesis. My findings confirm that normal growth of the embryonic ventricle is associated with a rapid increase in cardiomyocyte number, that was of 50% in the period 96-120 hpf, accompanied by increasing chamber trabeculation. This is also characterized by an increase in the gene expression of most of cardiac development relevant transcription factors, i.e. GATA4, 5 and 6, and MEF2c. The significant reduced cardiovascular function (14% of Ejection Fraction compared to 20% in controls) at 2 h post laser injury in the zebrafish embryonic heart promptly recovers at 24 hour post-laser, accompanied by acceleration of cardiomyocyte proliferation, that increased of 49% in injured ventricles compared to 20% in controls in the period 2-24 h post-laser. Pharmacological and genetic inhibition of CDK9 activity also significantly reduced cardiac growth, cardiomyocyte number, ventricle function and impairs functional recovery following laser injury. Conversely, genetic inhibition of LARP7, a CDK9 repressor, resulted in increased cardiomyocyte number and was associated with full functional and cellular recovery following laser-injury. In conclusion, I have provided evidence, in the zebrafish embryonic heart, that CDK9 plays an important role in cardiac growth and development and impacts significantly on cardiomyocyte proliferation. I have also shown that CDK9 manipulation significantly affects cellular and functional recovery following laser-induced injury. Further studies are required to further define the role of CDK9 and LARP7 in the heart and develop therapeutic strategies using this pathway that could contribute to cellular repair mechanisms in the adult mammalian heart.

Spinal cord injury, acute pain, and morphine tolerance are important issues in the clinical practice. A primary injury to the spinal cord causes both morphological and biochemical changes with initiation of the devastating secondary pathophysiological pathways that ultimately destroy CNS cells and cause degeneration of nerve fibers. Tissue injury is associated with sensitization of nociceptors and subsequent changes in the excitability of central neurons, known as central sensitization. Nociceptor sensitization and central sensitization are believed to underlie the development of primary and secondary hyperalgesia, respectively. The most efficacious drugs used to relieve pain are the opioid analgesics. Chronic administration leads to the development of tolerance. Tolerance is manifested as a decreased potency of the drug, so that progressively larger doses must be administered to achieve a given level of analgesia. The processes underlying opioid tolerance still need to be elucidated. Recently, it is found calpain-Cdk5 (cyclin-dependent kinase-5)-p35 pathway modulation implicated in neuroprotection, acute nociceptive response, and morphine analgesia. In this thesis, we evaluate calpain inhibitor-MDL28170 and Cdk5 inhibitor-roscovitine against rat spinal cord hemisection, formalin-induced acute nociceptive responses, and chronic morphine tolerance. We found calpain-Cdk5-p35 pathway inhibition could protect spinal cord hemisection and subsequent neurodegeneration, inhibit formalin-induced flinch response involving DARPP-32 (dopamine and c-AMP regulated phosphoprotein, MW=32 kDa) phosphorylation, and reverse right shifted morphine dose-response curve with upregulated ED50 (50% of effective dose) reduction. Taken together, calpain-Cdk5-p35 pathway inhibition is useful in the management of spinal cord injury, acute inflammatory pain, and attenuate morphine tolerance development with further clinical application.

Cyclin-dependent kinase-5 (Cdk5) was identified as a serine/threonine kinase that plays an important role in neuronal development. Association with one of the neuronal activators, p35 or p39, is required for Cdk5 to elicit its diverse effects in the nervous system, such as neurite outgrowth. In addition to these, increasing evidence suggests that Cdk5 also plays an important role in cocaine addiction, neurotransmitter release, NMDA receptor phosphorylation. This thesis is divided into three parts which deals with the effects of Cdk5 inhibitor¡Ðroscovitine on the morphine tolerance development, acute inflammatory pain, and pilocarpine-induced seizure respectively. The first part explored the effect of Cdk5 inhibitior¡Ðroscovitine on the morphine antinociceptive tolerance development. Delta FosB activation is involved in morphine tolerance. Cyclin-dependent kinase- 5 (Cdk5) is found to be the downstream target of delta FosB. We examined the effects of the potent selective Cdk5 inhibitor¡Ðroscovitine on the development of antinociceptive tolerance of morphine. Tolerance was induced by continuous infusion of morphine 5 µg/hr intrathecally (i.t.) for 5 days. The effect of co-administration of roscovitine 1 µg/hr i.t. for 5 days was also examined. Roscovitine co-administration enhanced the antinociceptive effect of morphine in morphine tolerant rats. It also shift the morphine antinociceptive dose¡Ðresponse curve to the left during morphine tolerance induction, and reduced the increase in the ED50 of morphine two-fold. Collectively, these findings suggest Cdk5 modulation may be involved in the development of morphine tolerance and its inhibitor will enhance antinociceptive effect. The second part discussed the roscovitine effect on acute inflammatory pain. Formalin injected into the rat hind paw will evoke flinching (consisting of an elevation and shrinking back of the injected paw), a reliable parameter of pain behavior. The nociceptive response to formalin occurs in a biphasic pattern: there isan initial acute period (phase 1), and after a short period of remission, phase 2 begins and consists of a longer period (1 hour) of sustained activity. The initial response was initially attributed to a direct algogenic effect of formalin, whereas phase 2 was associated with the central sensitization. In this study, the Cdk5 inhibitor¡Ðroscovitine was injected intrathecally to elucidate the mechanism of Cdk5 activation during formalin-induced hyperalgesia. The 50 ul of 5% formalin solution was used as the noxious stimulant. The rats were injected with 0, 50, 100, and 200ug roscovitine intrathecally thirty minutes before hind paw formalin injection. Intrathecal 200ug roscovitine injection attenuates the phase I flinch response. And intrathecal 50, 100, and 200ug roscovitine injection suppress phase II flinch response effectively. Roscovitine administration could effectively suppress the formalin-induced flinch behavior. This implies the activation of Cdk5 plays an important role in the sensitization after nociceptive stimulation. The third part focus on the roscovitine effect on the pilocarpine induced seizure. Pilocarpine temporal lobe epilepsy model is widely used. Chronic electroconvulsive therapy could upregulate Cdk5 activity. Cdk5 inhibitor¡Ðroscovitine could suppress NMDA induced long-term potentiation in hippocampal slice. Intracerebroventricular injection of 100£gg roscovitine 30 min before pilocarpine-induced epilepsy could significantly decrease the seizure-induced mortality ( 11% in roscovitine group VS 77% in control group). The escape latency, spatial memory impairment, in the pilocarpine-induced seizure group is significant longer than the roscovitine pretreatment group in the Morris water maze test after one month (p¡Õ0.05). It is concluded Cdk5 may play an important in the pathogenesis of epilepsy. Therefore, Cdk5 inhibition may become another way for the epilepsy treatment.

Dissertation (Ph.D.).--University of Texas Graduate School of Biomedical Sciences at San Antonio, 2007. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--Cornell University, May, 2008. / Vita. Includes bibliographical references (leaves 140-170).