A novel strategy for inhibiting growth of human pancreatic cancer cells by blocking cyclin-dependent kinase activity

Network controllability solutions for computational drug repurposing using genetic algorithms

Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over the dynamics of a given network, a problem known as network controllability. We propose in this article a new solution for this problem based on genetic algorithms. We tailor our solution for applications in computational drug repurposing, seeking to maximize its use of FDA-approved drug targets in a given disease-specific protein-protein interaction network. We demonstrate our algorithm on several cancer networks and on several random networks with their edges distributed according to the Erdős-Rényi, the Scale-Free, and the Small World properties. Overall, we show that our new algorithm is more efficient in identifying relevant drug targets in a disease network, advancing the computational solutions needed for new therapeutic and drug repurposing approaches.

Identification of key microRNAs and their targets in exosomes of pancreatic cancer using bioinformatics analysis

Pancreatic cancer (PC) is one of the most lethal tumors, due to late diagnosis and limited surgical strategies. It has been reported that serum exosomal microRNAs (S-Exo-miRNAs) play a pivotal role as signaling molecules and serve as noninvasive diagnosis methods for PC. The combination of S-Exo-miRNAs with the corresponding target also plays an important role in the tumor microenvironment.Here we investigated S-Exo-miRNAs involved in PC. The gene expression profile was downloaded from the Gene Expression Omnibus (GEO) database. The analysis was carried out using GEO2R. The targets of differentially expressed serum exosomal miRNAs (DE-S-Exo-miRNAs) were predicted by 4 bioinformatic algorithms (miRanda, miRDB, miRWalk, and Targetscan). Further analysis with gene ontology (GO) and Kyoto Encyclopedia of Genomes pathway (KEGG) enrichment analyses were performed with Cytoscape software version 3.4.0. Subsequently, the interaction regulatory network of target genes was performed with the Search Tool for the Retrieval of Interacting Genes (STRING) database (http://www.string-db.org/) and visualized using Cytoscape software.We downloaded the gene expression profile GSE50632, which was based on an Agilent microarray GPL17660 platform containing 4 eligible samples. In total 467 DE-S-Exo-miRNAs were obtained, including 7 overexpressed miRNAs (1.50%), and 460 remaining underexpressed miRNAs (98.50%). The databases miRWalk, miRDB, miRanda, and TargetScan were used to predict their potential targets, which were subsequently submitted to Cytoscape software version 3.4.0 (www.cytoscape.org). Next the functional and pathway enrichment analysis were used for the KEGG pathway and GO categories analysis. The enrichment analysis identified the genes involved in such processes as developmental and negative regulation of multicellular organismal processes, regulation of anatomical structure morphogenesis, regulation of cell death, apoptotic processes and mitogen-activated protein kinase (MAPK) signaling pathway, transforming growth factor - beta (TGF -β) signaling pathway, cyclic adenosine monophosphate (cAMP) signaling pathway, and the phosphatidylinositol-3 kinases/Akt (PI3K-Akt) signaling pathway. Subsequently according to the protein-protein interaction (PPI) network, the top 10 genes were obtained. The enrichment analyses of the genes involved in a significant module revealed that these genes were related to the TGF-β signaling pathway. After reviewing the literature, we identified the apoptosis genes, and their corresponding miRNAs that have a relationship with apoptosis of the tumor.This analysis provides a comprehensive understanding of the roles of S-Exo-miRNAs and the related targets in the development of PC. Additionally, the present study provides promising candidate targets for early diagnosis and therapeutic intervention. However, these predictions require further experimental validation in future studies.

Discovery and development of Seliciclib. How systems biology approaches can lead to better drug performance

Seliciclib (R-Roscovitine) was identified as an inhibitor of CDKs and has undergone drug development and clinical testing as an anticancer agent. In this review, the authors describe the discovery of Seliciclib and give a brief summary of the biology of the CDKs Seliciclib inhibits. An overview of the published in vitro and in vivo work supporting the development as an anti-cancer agent, from in vitro experiments to animal model studies ending with a summary of the clinical trial results and trials underway is presented. In addition some potential non-oncology applications are explored and the potential mode of action of Seliciclib in these areas is described. Finally the authors argue that optimisation of the therapeutic effects of kinase inhibitors such as Seliciclib could be enhanced using a systems biology approach involving mathematical modelling of the molecular pathways regulating cell growth and division.

Cyclin-dependent kinase inhibitors and the treatment of gastrointestinal cancers

The cell cycle is a highly conserved and tightly regulated biological system that controls cellular proliferation and differentiation. The cell cycle regulatory proteins, which include the cyclins, the cyclin-dependent kinases (CDKs), and the CDK inhibitors, are critical for the proper temporal and spatial regulation of cellular proliferation. Conversely, alterations in cell cycle regulatory proteins, leading to the loss of normal cell-cycle control, are a hallmark of many cancers, including gastrointestinal cancers. Accordingly, overexpression of CDKs and cyclins and by contrast loss of CDK inhibitors, are all linked to gastrointestinal cancers and are often associated with less favorable prognoses and outcomes. Because of the importance that the cell cycle regulatory proteins play in tumorigenesis, currently there is a broad spectrum of cell-cycle inhibitors under development that, as a group, hold promise as effective cancer treatments. In support of this approach to cancer treatment, the growing availability of molecular diagnostics techniques may help in identifying patients who have driving abnormalities in the cell-cycle machinery and are thus more likely to respond to cell-cycle inhibitors. In this review, we discuss the prevalence of cell-cycle abnormalities in patients with gastrointestinal cancers and provide a preclinical and clinical overview of new agents that target cell-cycle abnormalities with a special emphasis on gastrointestinal cancers.

Translational advances and novel therapies for pancreatic ductal adenocarcinoma: hope or hype?

Biological complexity, inaccessible anatomical location, nonspecific symptoms, lack of a screening biomarker, advanced disease at presentation and drug resistance epitomise pancreatic ductal adenocarcinoma (PDA) as a poor-prognosis, lethal disease. Twenty-five years of research (basic, translational and clinical) have barely made strides to improve survival, mainly because of a fundamental lack of knowledge of the biological processes initiating and propagating PDA. However, isolation of pancreas cancer stem cells or progenitors, whole-genome sequencing for driver mutations, advances in functional imaging, mechanistic dissection of the desmoplastic reaction and novel targeted therapies are likely to shed light on how best to treat PDA. Here we summarise current knowledge and areas where the field is advancing, and give our opinion on the research direction the field should be focusing on to better deliver promising therapies for our patients.

Mesothelin-induced pancreatic cancer cell proliferation involves alteration of cyclin E via activation of signal transducer and activator of transcription protein 3

Mesothelin (MSLN) is a cell surface glycoprotein that is overexpressed in human pancreatic cancer. Although its value as a tumor marker for diagnosis and prognosis and as a preferred target of immunointervention has been evaluated, there is little information on the growth advantage of MSLN on tumor cells. In this study, we examined the effect of MSLN on pancreatic cancer cell proliferation, cell cycle progression, expression of cell cycle regulatory proteins, and signal transduction pathways in two pancreatic cancer cell lines, MIA-MSLN (overexpressing MSLN in MIA PaCa-2 cells) and BxPC-siMSLN (silencing MSLN in BxPC-3 cells). Increased cyclin E and cyclin-dependent kinase 2 expression found in MIA-MSLN cells correlated with significantly increased cell proliferation and faster cell cycle progression compared with control cells. BxPC-siMSLN cells showed slower proliferation and slower entry into the S phase than control cells. Signal transducer and activator of transcription protein 3 (Stat3) was constitutively activated in MIA-MSLN cells, but not in control cells. Inhibition of Stat3 activation in MIA-MSLN cells by the Janus-activated kinase-selective inhibitor tyrphostin AG490 was followed by a marked decrease in proliferation of the cells. Small interfering RNA against Stat3 significantly reduced the MIA-MSLN cell cycle progression with a concomitant decrease in cyclin E expression. Our data indicate that overexpression of MSLN in pancreatic cancer cells leads to constitutive activation of the transcription factor Stat3, which results in enhanced expression of cyclin E and cyclin E/cyclin-dependent kinase 2 complex formation as well as increased G(1)-S transition.

The separation of antagonist from agonist effects of trisubstituted purines on CaV2.2 (N-type) channels

Dihydropyridines can affect L-type calcium channels (CaV1) as either agonists or antagonists. Seliciclib or R-roscovitine, a 2,6,9-trisubstituted purine, is a potent cyclin-dependent kinase inhibitor that induces both agonist and antagonist effects on CaV2 channels (N-, P/Q- and R-type). We studied the effects induced by various trisubstituted purines on CaV2.2 (N-type) channels to learn about chemical structure-function relationships. We found that S-roscovitine and R-roscovitine showed similar potency to inhibit, but agonist activity of S-roscovitine required at least a 20-fold higher concentration, suggesting stereospecificity of the agonist-binding site. The testing of other trisubstituted purines showed a correlation between CaV2.2 inhibition and cyclin-dependent kinase affinity that broke down after determining that a chemically unrelated inhibitor, kenpaullone, was a poor CaV2.2 inhibitor, and a kinase inactive analog (dimethylamino-olomoucine; DMAO) was a strong inhibitor, which together support a kinase independent effect. In fact, like dihydropyridine-induced L-channel inhibition, R-roscovitine left-shifted the closed-state inactivation versus voltage relationship, which suggests that inhibition results from CaV2 channels moving into the inactivated state. Trisubstituted purine antagonists could become clinically important drugs to treat diseases, such as heart failure and neuropathic pain that result from elevated CaV2 channel activity.

Roscovitine differentially affects CaV2 and Kv channels by binding to the open state

Roscovitine potently inhibits cyclin-dependent kinases (CDK) and can independently slow the closing of neuronal (CaV2.2) calcium channels. We were interested if this drug could affect other ion channels similarly. Using whole cell recordings, we found that roscovitine specifically slows deactivation of all CaV2 channels (N, P/Q and R) by binding to the open state. This effect had a rapid onset and EC(50)=54, 120 and 54microM for N-, P/Q-, and R-type channels, respectively. Deactivation of other channel types was not slowed, including L-type calcium channels (CaV1.2, CaV1.3), potassium channels (native, Kv4.2, Kv2.1 and Kv1.3), and native sodium channels. However, most of the channels tested were inhibited by roscovitine. The inhibition was characterized by slow development and a lower affinity (EC(50)=100-300microM). Surprisingly, potassium channels were rapidly inhibited with an EC(50)=23microM, which is similar to the EC(50) for roscovitine block of cell division [Meijer, L., Borgne, A., Mulner, O., Chong, J., Blow, J., Inagaki, N., Inagaki, M., Delcros, J., Moulinoux, J., 1997. Biochemical and cellular effects of roscovitine, a potent and selective inhibitor of the cyclin-dependent kinases cdc2, cdk2 and cdk5. Eur. J. Biochem. 243, 527-536]. Potassium current inhibition seemed to result from open channel block. The high potency of these two rapid onset effects makes them complicating factors for ongoing clinical trials and research using roscovitine. Thus, the physiology and pharmacology of slow CaV2 deactivation and potassium channel block must be explored.

Explant-induced reactivation of herpes simplex virus occurs in neurons expressing nuclear cdk2 and cdk4

Herpes simplex virus (HSV) establishes productive (lytic) infections in nonneuronal cells and nonproductive (latent) infections in neurons. It has been proposed that HSV establishes latency because quiescent neurons lack cellular factors required for productive infection. It has been further proposed that these putative factors are induced following neuronal stress, as a requirement for HSV reactivation. To date, the identity of these putative cellular factors remains unknown. We have demonstrated that cyclin-dependent kinase (cdk) 1, 2, or 7 is required for HSV replication in nonneuronal cells. Interestingly, cdks 1 and 2 are not expressed in quiescent neurons but can be induced in stressed neurons. Thus, cdks may be among the cellular proteins required for HSV reactivation whose neuronal expression is differentially regulated during stress. Herein, we determined that neuronal expression of nuclear cdk2, cdk4, and cyclins E and D2 (which activate cdks 2 and 4, respectively) was induced following explant cultivation, a stressful stimulus that induces HSV reactivation. In contrast, neuronal expression of cdk7 and cytoplasmic cdk4 decreased during explant cultivation, whereas cdk3 was detected in the same small percentage of neurons before and after explant cultivation and cdks 1, 5, and 6 were not detected in neuronal cell bodies. HSV-1 reactivated specifically in neurons expressing nuclear cdk2 and cdk4, and an inhibitor specific for cdk2 inhibited HSV-1 reactivation. We conclude that neuronal levels of cdk2 are among the factors that determine the outcome of HSV infections of neurons.