Recent Developments in Cancer Systems Biology

This ebook includes original research articles and reviews to update readers on the state of the art systems approach to not only discover novel diagnostic and prognostic biomarkers for several cancer types, but also evaluate methodologies to map out important genomic signatures. In addition, therapeutic targets and drug repurposing have been emphasized for a variety of cancer types. In particular, new and established researchers who desire to learn about cancer systems biology and why it is possibly the leading front to a personalized medicine approach will enjoy reading this book

Characterization and therapeutic exploitation of molecular vulnerabilities in genetically defined lung cancer

Lung cancer is one of the most common cancer types and responsible for the largest number of cancer-related deaths worldwide. Typically, lung cancer arises in individuals with heavy smoking background and only rarely in never-smokers. Various cells of origin within the lung give rise to distinct, molecularly heterogenous lung cancer subtypes with the two major subtypes non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). Targeted therapy options also vary significantly between the specific subtypes and while oncogene-driven lung adenocarcinoma (LUAD) is already successfully treated with targeted drugs, no targeted therapies are available in SCLC. LUAD is often driven genetic alterations such as point mutations and rearrangements in genes of receptor tyrosine kinases (RTKs) like EGFR leading to aberrant activation of receptor tyrosine kinase signaling and oncogenic transformation. Mutation-selective small molecule RTK inhibitors have been developed to specifically kill oncogene-addicted cancer cells. Introduction of third generation EGFR inhibitor osimertinib substantially increased survival of EGFR-mutant LUAD patients but on-target resistance mutations such as EGFR G724S limit osimertinib efficacy leading to tumor relapse. Remarkably, we observed that second-generation EGFR inhibitor afatinib displayed selective activity against EGFR G724S in cell line and animal models. In contrast to osimertinib, afatinib still binds to EGFR G724S and reduces cellular viability, EGFR signaling, transformation and in vivo growth of EGFR G724S cells, therefore providing a possible treatment strategy for patients that relapse after osimertinib treatment due to EGFR G724S. Oncogenic gene fusions involving RET also lead to cellular transformation and LUAD tumorigenesis. Previously, multi-kinase inhibitors were used to treat RET-rearranged cancers with limited success due to lack of RET-specificity and RET gatekeeper mutations impeding inhibitor binding. We identified AD80, a type II kinase inhibitor that binds RET in the DFG-out conformation. AD80 displayed selective activity against common RET fusions KIFB-RET and CCDC6-RET and retained activity against RET V804M gatekeeper mutation. AD80 efficiently reduced RET- and downstream signaling as well as RET-associated gene expression. AD80 also displayed in vivo efficacy in CCDC6-RET patient-derived xenograft (PDX) models, demonstrating the potential of type II inhibitors as targeted therapy against RET-rearranged LUAD. In contrast to NSCLC, SCLC is defined by inactivation of tumor suppressors TP53 and RB1 and lacks targetable oncogenic drivers. Frequent activation of MYC transcription factor family members (MYC, MYCL, and MYCN) further accelerate tumor growth and aggressiveness. We found that activation of individual MYC family members entails differential molecular vulnerabilities. MYC overexpression is associated with high levels of DNA damage, repression of BCL2 expression and high apoptotic priming, leading to higher sensitivity towards Aurora kinase and MCL1 inhibition whereas high MYCL/MYCN expression is associated with resistance against these perturbations. Our study highlights that MYC status can be predictive for therapy response and might be used for molecularly-guided, patient stratification for future targeted therapy regimens in SCLC. A rare but very aggressive lung cancer type, NUT carcinoma is driven by BRD4-NUT fusion protein leading to large-scale epigenetic reprogramming and deregulated transcription of genes driving tumorigenesis. Using high-throughput viability screening, we identified that NUT carcinoma cells are preferentially sensitive against CDK9 inhibition. We observed, that CDK9 inhibition increases RNA Polymerase II pausing possibly reverting BRD4-NUT-mediated, transcriptional activation of pro-tumor genes warranting further investigation of CDK9 inhibition in NUT carcinoma

Boolean Networks as Predictive Models of Emergent Biological Behaviors

Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory networks to species in ecological networks) and the often-incomplete state of system knowledge (e.g., the unknown values of kinetic parameters for biochemical reactions). Boolean networks have emerged as a powerful tool for modeling these systems. We provide a methodological overview of Boolean network models of biological systems. After a brief introduction, we describe the process of building, analyzing, and validating a Boolean model. We then present the use of the model to make predictions about the system's response to perturbations and about how to control (or at least influence) its behavior. We emphasize the interplay between structural and dynamical properties of Boolean networks and illustrate them in three case studies from disparate levels of biological organization.Comment: Review, to appear in the Cambridge Elements serie

Validation of synthetic lethal hits of microtubule targeting agents

Les microtubules, composants clés du cytosquelette des cellules eucaryotes, sont des polymères de tubuline très dynamiques et impliqués dans une grande variété de processus cellulaires. Leur rôle essentiel dans le cycle cellulaire a fait d’eux une cible validée en thérapie anticancéreuse. Malgré l’efficacité clinique des agents ciblant les microtubules (ACM), les effets secondaires compliquent l’utilisation. Nous avons cherché à identifier des vulnérabilités génétiques qui peuvent être exploitées pour diminuer la dose requise tout en maintenant l'efficacité, et donc réduire les effets secondaires. En collaboration avec le laboratoire Tyers à l’IRIC, nous avons réalisé un criblage génétique basé sur la létalité synthétique avec des agents antiprolifératifs, dont les ACMs. Nous avons sélectionné les gènes dont l’extinction sensibilisait les cellules aux ACMs. J’ai confirmé que l’invalidation de chacun des gènes GNA13, SEPHS1, DLGAP5 et des gènes QRICH1, DLGAP5 sensibilisaient les cellules NALM6 au docétaxel et la vincristine respectivement. En revanche, aucune invalidation de ces gènes n'a augmenté la sensibilité au docétaxel dans les cellules U2OS. En plus de son effet avec le docétaxel, le gène GNA13 s’est distingué être une cible particulièrement intéressante. En effet, la perte complète de GNA13 augmente considérablement la fréquence et la gravité d’erreurs de ségrégation des chromosomes dans les cellules U2OS. Cette augmentation n’a pas été rectifiée à la suite d’un traitement avec la molécule UMK57, connue pour réduire le taux d’erreurs de ségrégation des chromosomes. De manière intéressante, la perte complète de GNA13 augmente également la fréquence des erreurs de ségrégation des chromosomes dans les cellules RPE1, cellules non-cancéreuses et stables au niveau chromosomique. Cela suggère que la perte complète de GNA13 ne nécessite pas de transformation ni d'instabilité chromosomique, comme conditions préalables pour exacerber l'instabilité chromosomique. L’ensemble de ces résultats ouvre une nouvelle voie de stratégies thérapeutiques anticancéreuses, à savoir, le traitement des cancers présentant une mutation des gènes QRICH1, DLGAP5, GNA13, et SEPHS1 avec de faibles doses d’ACMs. En particulier, GNA13 est fréquemment muté dans certains lymphomes. De plus, les résultats obtenus démontrent que la perte complète de GNA13 aggrave l’instabilité chromosomique et par conséquent, pourrait être impliquée dans la cancérogenèse.Microtubules, key components of the eukaryotic cytoskeleton, are highly dynamic polymers of tubulin implicated in a wide variety of cellular processes. Their essential roles in the cell cycle have made them a valid target in cancer therapy. Despite the clinical efficacy of microtubule targeting agents (MTA), their use is hampered by side effects. We sought to identify genetic vulnerabilities that can be exploited to decrease the required dose while maintaining efficacy, and therefore reduce side effects. In collaboration with the Tyers laboratory at IRIC, we carried out a genetic screen based on synthetic lethality with antiproliferative agents, including MTAs. We have selected genes whose knockout sensitized cells to MTAs. I have confirmed that the knockout of GNA13, SEPHS1, DLGAP5, and QRICH1, DLGAP5, sensitize NALM6 cells to docetaxel and vincristine respectively. However, no knockout of these genes increased the sensitivity to docetaxel in U2OS cells. In addition to its effect with docetaxel, GNA13 stood out as being a particularly exciting target. GNA13 knockout increased the frequency and severity of chromosome segregation errors in U2OS cells. This increase was not corrected following treatment with UMK57, a molecule known to reduce the rate of chromosome segregation errors. Interestingly, the GNA13 knockout also increased the frequency of chromosome segregation errors in non-cancerous and chromosomally stable RPE1 cells. This suggests that GNA13 does not require transformation nor chromosomal instability as prerequisites for exacerbating chromosomal instability. Overall, these results open up a new avenue of anticancer therapeutic strategies, namely, the treatment of cancers presenting mutations in QRICH1, DLGAP5, GNA13, and SEPHS1 with lower doses of MTAs. In particular, GNA13 is frequently mutated in certain lymphomas. In addition, the results obtained demonstrate that GNA13 knockout exacerbates chromosomal instability and, therefore, could be involved in carcinogenesis

MicroRNA and Cancer

MicroRNAs (miRs) are small noncoding RNAs that function as post-transcriptional regulators of gene expression and have important roles in almost all biological pathways. Deregulated miR expression has been detected in numerous cancers, where miRs act as both oncogene and tumor suppressors. Due to their important roles in tumorigenesis, miRs have been investigated as prognostic and diagnostic biomarkers and as useful targets for therapeutic intervention. From a therapeutic point of view, two modalities can serve to rectify gene networks in cancer cells. For oncomiRs, a rational means is downregulation through antagomirs. Moreover, observations of the pathological reductions in tumor-suppressive miRs have inspired the concept of “miR replacement therapy” to enhance the amount of these miRs, thereby restoring them to normal levels. However, the clinical applicability of miR-based therapies is severely limited by the lack of effective delivery systems. Therefore, to understand the role of this new class of regulators, we need to identify the mRNA targets regulated by individual miRs as well as to develop specific, efficient, and safe delivery systems for therapeutic miRs

New Prognostic and Predictive Markers in Cancer Progression

Biomarkers are of critical medical importance for oncologists, allowing them to predict and detect disease and to determine the best course of action for cancer patient care. Prognostic markers are used to evaluate a patient’s outcome and cancer recurrence probability after initial interventions such as surgery or drug treatments and, hence, to select follow-up and further treatment strategies. On the other hand, predictive markers are increasingly being used to evaluate the probability of benefit from clinical intervention(s), driving personalized medicine. Evolving technologies and the increasing availability of “multiomics” data are leading to the selection of numerous potential biomarkers, based on DNA, RNA, miRNA, protein, and metabolic alterations within cancer cells or tumor microenvironment, that may be combined with clinical and pathological data to greatly improve the prediction of both cancer progression and therapeutic treatment responses. However, in recent years, few biomarkers have progressed from discovery to become validated tools to be used in clinical practice. This Special Issue comprises eight review articles and five original studies on novel potential prognostic and predictive markers for different cancer types

Novel Anti-cancer Agents and Cellular Targets and Their Mechanism(s) of Action

Patient outcomes remain poor for many cancers despite improvements in treatments and new molecular-targeted biomedicines for certain cancer types or subtypes. Dose-limiting toxicity, a narrow therapeutic index, and the development of resistance to traditional anti-cancer agents are well-established. It is apparent that inherent and acquired drug resistance are major challenges with molecular-targeted agents and that on- as well as off-target side effects can still occur. Other issues include drug metabolism by the body and safely supplying a sufficient amount of active drug to the tumor cells. There is a clear and urgent need for new molecular targets and drugs that specifically target cancer cells in different ways to existing approved drugs. This book, through a collection of eight research articles and two review articles from the Biomedicines themed Special Issue ‘Novel Anti-Cancer Agents and Cellular Targets and Their Mechanism(s) of Action’, provides a snapshot of some of the diverse and exciting research approaches being taken by the cancer research community in trying to address some of these therapeutic challenges

CELL CYCLE AND APC/C UBIQUITYLATION REGULATE CHROMATIN DYNAMICS TO ACHIEVE TIMELY CELL PROLIFERATION

Cell cycle progression is an intricately controlled, temporally regulated biological process that involves multiple regulators, both transcriptionally and post-transcriptionally to integrate diverse signaling pathways to facilitate productive cell proliferation. A combination of oscillatory gene transcription, cyclin phosphorylation of downstream targets, and APC/C-mediated ubiquitylation governs the cell cycle program. Importantly, the epigenome also influences cell proliferation through structural compaction that controls transcription factor access to the DNA (for cell cycle gene expression and histone biogenesis), regulates DNA replication timing, and facilitates chromosomal condensation for mitotic segregation. Similarly, the cell cycle regulates the epigenetic environment through histone transcription, origin licensing and firing, chromosomal condensation and segregation, cell cycle regulated histone/DNA post-translational modifications, and manipulation of chromatin modifiers’ expression and stability. Significantly, cell proliferation dynamics are aberrantly regulated in cancer and other genetic diseases. The central finding of this research project shows that APC/C-Cdh1 ubiquitylation controls many epigenetic regulators that are implicated in cell cycle progression. In particular, we characterize the KEN-dependent APC/C-Cdh1-mediated proteasomal degradation of UHRF1. UHRF1 is a critical epigenetic modifier that coordinates DNA methylation maintenance during S phase and is an oncogene that is overexpressed in many cancers. We discovered that in contrast to wild-type UHRF1, a non-degradable version of UHRF1 stably expressed in cells binds less well to the Cdh1 co-activator and is not robustly ubiquitylated at mitotic exit. These cells also enter S phase more rapidly and have upregulated cyclin E levels. Furthermore, lack of UHRF1 degradation induces hypermethylation of early replicating regions and hypomethylation of late replicating sites of the genome. This work provides mechanistic insight into how UHRF1 itself is regulated during cell cycle progression, an area which remains largely understudied in the field.Doctor of Philosoph

Promocijas darbs

Elektroniskā versija nesatur pielikumusSīkšūnu plaušu vēzis (SŠPV) ir visagresīvākais plaušu vēža paveids, kur ķīmijterapija ļauj ievērojami pagarināt pacienta dzīvi un samazināt slimības simptomus. Daudzos gadījumos ir iespējama pilnas remisijas sasniegšana. Tomēr metastātisku SŠPV uzskata par neizārstējamu slimību, jo praktiski vienmēr audzējs recidivē un kļūst neuzņēmīgs pret specifisko terapiju. Vēža cilmes šūnas var būt atbildīgas par SŠPV recidīvu un rezistences attīstību. Hedgehog signālceļš regulē vairākus ar cilmšūnām un proliferāciju saistītus gēnus, tādējādi veicinot cilmšūnu un audu progenitoro šūnu izdzīvošanu un proliferāciju. Darba mērķis. Pierādīt, ka klīniskajiem parametriem un Sonic Hedgehog (Shh) embrioģenēzi regulējošā signālceļa aktivitātei ir prognostiska nozīme sīkšūnu plaušu vēža pacientiem, kā arī izvērtēt iespējamo signālceļa saistību ar rezistences veidošanos.Small cell lung cancer (SCLC) is the most aggressive type of lung cancer where chemotherapy allows to prolong the life of the patient and reduce the symptoms of the disease significantly. Complete remission is possible in many cases. However, metastatic SCLC is considered to be an incurable disease because the tumour almost always recurs and becomes resistant to the specific treatment. Cancer stem cells may be responsible for the recurrence of SCLC and development of resistance. The Hedgehog signalling pathway regulates several genes associated with stem cells and proliferation, thus promoting the survival and proliferation of stem cells and tissue progenitor cells. Research Objective. To demonstrate that clinical parameters and the activity of the Sonic Hedgehog (Shh) embryonic signalling pathway are of prognostic relevance in small cell lung cancer patients and to evaluate the possible association of the signalling pathway with the development of resistanc