Advocating the need of a systems biology approach for personalised prognosis and treatment of B-CLL patients

The clinical course of B-CLL is heterogeneous. This heterogeneity leads to a clinical dilemma: can we identify those patients who will benefit from early treatment and predict the survival? In recent years, mathematical modelling has contributed significantly in understanding the complexity of diseases. In order to build a mathematical model for determining prognosis of B-CLL one has to identify, characterise and quantify key molecules involved in the disease. Here we discuss the need and role of mathematical modelling in predicting B-CLL disease pathogenesis and suggest a new systems biology approach for a personalised therapy of B-CLL patients

Biological Networks

Networks of coordinated interactions among biological entities govern a myriad of biological functions that span a wide range of both length and time scales—from ecosystems to individual cells and from years to milliseconds. For these networks, the concept “the whole is greater than the sum of its parts” applies as a norm rather than an exception. Meanwhile, continued advances in molecular biology and high-throughput technology have enabled a broad and systematic interrogation of whole-cell networks, allowing the investigation of biological processes and functions at unprecedented breadth and resolution—even down to the single-cell level. The explosion of biological data, especially molecular-level intracellular data, necessitates new paradigms for unraveling the complexity of biological networks and for understanding how biological functions emerge from such networks. These paradigms introduce new challenges related to the analysis of networks in which quantitative approaches such as machine learning and mathematical modeling play an indispensable role. The Special Issue on “Biological Networks” showcases advances in the development and application of in silico network modeling and analysis of biological systems

Development and validation of kinase activity reporters for the dynamic study of cell response modalities by microscopy

Necroptosis is defined as a caspase-independent programmed cell death and relies on a signaling pathway involving two serine-threonine kinases: Receptor-Interacting Protein Kinase 1 and 3 (RIPK1 and RIPK3) and the pseudo-kinase Mixed-Lineage Kinase Like (MLKL). Activation of Extracellular signal-Regulated Kinases 1 and 2 (ERK1/2) was reported to be involved in different modes of programmed cell death. It is now accepted that the regulation of the duration, magnitude and subcellular compartmentalization of ERK1/2 activity by specific spatio-temporal regulators is interpreted by the cell towards cell fate determination. ERK1/2 inhibition delays TNFα-induced necroptosis in L929 cells in a dose dependent manner but did not block it, providing arguments for a pro-necrotic function of ERK1/2. In this context, a compartmentalized biphasic phosphorylation of ERK1/2 was observed. Our results indicate a RIPK1-dependent phosphorylation of ERK1/2. Owing to the importance of ERK1/2 spatio-temporal dynamics in determining cellular responses, we developed a new reporter of ERK2 localization named ERK2-LOC. We observed a transient translocation of ERK2 when necroptosis was triggered in L929 upon TNFα stimulation, followed by progressive ERK2 accumulation in the nucleus. ERK1/2 activities were monitored during necroptosis using a FRET-based kinase biosensor for ERK1/2 (ERK1/2-ACT). Using ERK1/2-ACT, a dedicated spatio-temporal signature of ERK1/2 activity was recorded during necroptosis. Finally, to correlate ERK1/2 activity code with necroptosis occurrence, we also engineered a first generation of FRET biosensors to report on both RIPK1 and RIPK3 activities during necroptosis

Mitochondrial Morphology Dynamics during Apoptosis - An integrative modeling approach

Mitochondria are central to many important cellular functions. The entire mitochondrial population is in constant flux, driven by continuous fusion and division of mitochondria. Defects in mitochondrial dynamics can cause deficits in mitochondrial respiration, morphology and motility leading to apoptosis under extreme conditions. An important and still unresolved question is how the heterogeneity of mitochondrial morphology, distribution and function are mechanistically realized in the cell. Importantly, to what extent is mitochondrial morphology dependent or affects cell fate decisions. Despite the intense focus on unraveling connections between mitochondrial morphology and severe human pathologies, the analysis and systematic description of mitochondrial phenotypes remains an open challenge. Current approaches to study mitochondrial morphology are limited by low data sampling coupled to manual identification and simplistic classification of complex morphological phenotypes. The overall goal of this work was to elucidate the nature of the relationship between mitochondria morphology and apoptotic events. Diverse apoptotic triggers were systematically tested and data concerning mitochondrial phenotypes and injury was collected to infer cause and consequence relationships. Therefore, high-resolution fluorescence imaging was employed to extract high-content information essential to identify and quantify spatial and conformational events in the single cell. These included monitoring of mitochondrial membrane permeability and quantification of Bax activation under matched conditions to assess mitochondrial stress. Experimentally, mitochondrial morphological transitions were followed in human breast carcinoma MCF-7 cells by tagging a mitochondrial inner membrane protein with a fluorescent probe. We made use of apoptotic conditions that have been previously reported to cause mitochondrial fragmentation or swelling. Wide field microscopy allowed for the collection of images containing cells with mostly networked, fragmented or swollen mitochondria. Next, image analysis was performed to extract several mitochondrial features that better characterize each class. These were grouped and used to build a decision tree-based classifier that automatically classifies individual mitochondria into the correspondent phenotypic class. Our population-based classifier accounts for intracellular sub-classes, intermediate mitochondrial stages and reproduces intercellular variances with high accuracy. Our results show that distinct apoptotic stimuli lead to subtle but significant differences in mitochondrial morphology within cell population that can be specific to a particular insult. Interestingly, there was no direct relation between the induced-mitochondrial classes and the analyzed apoptotic steps. In fact, some apoptotic drugs, which are known to cause similar mitochondrial damage, showed distinct mitochondrial morphology. Therefore, the observed heterogeneous response of mitochondria to stress strongly suggests that more complex, non-linear interactions exist. Here, we propose an integrated mechanistic and data-driven modeling approach to analyze heterogeneously quantified datasets and infer hierarchical interactions between mitochondrial morphology and apoptotic events. Our modeling results suggest that Bax activation leads to mitochondrial fragmentation, which is strongly associated with mitochondrial membrane depolarization events. In turn, the loss of mitochondrial membrane potential is closely related to mitochondrial swelling. Our model predictions are in accordance with previous published results and thereby validate our modeling approach that can now be easily extended to include new datasets. Surprisingly, mitochondrial fragmentation was not the most prominent phenotype, even under conditions where Bax activation was considerably high. Instead, swollen-mitochondria seem to be closer related to mitochondrial-associated death pathways. Next steps include the extension of our pipeline in a time-resolved manner and combined datasets acquisition in order to further investigate this hypothesis. In summary, we have established and validated a platform for mitochondrial morphological and functional analysis that offers results in an unbiased, systematic and statistically relevant manner. We believe the developed platform is suitable to be extensively used in the investigation of specific molecular targets. Possible applications include RNAi screens (e.g. morphology proteins) or extended compound libraries in a high-throughput mode. Importantly, it can now be further adjusted to other studies relevant to mitochondrial programmed cell death that will hopefully lead into the better understanding of mitochondrial role in physiology and disease progression

Systems microscopy to unravel cellular stress response signalling in drug induced liver injury

Toxicological insults are met by cellular adaptive stress response pathway activation. We find that activation of adaptive stress responses occur well before the typical ultimate outcome of chemical cell injury. To increase our understanding of chemically-induced adaptive stress response pathway activation and its contribution to safety assessment we believe that a time-resolved, sensitive and multiplex readout of chemical-induced toxicological relevant cellular stress responses will be essential. For that purpose, we developed a platform containing a panel of distinct adaptive stress response reporter cell lines. These are used for automated high content live cell imaging and quantitative multi-parameter image analysis to elucidate critical adaptive stress response pathway activation that can contribute to human chemical safety assessment. To conserve the endogenous gene regulatory programs, we tag selected reporter target genes with GFP using BAC-transgenomics approaches. In this thesis we demonstrate the functionality of individual BAC-GFP pathway in toxicity reporter cell lines. The application of these reporters in chemical safety assessment in relation to drug-induced liver injury is discussed in detail. We anticipate that ultimately a phenotypic adaptive stress response profiling platform will allow a high throughput and time-resolved classification of chemical-induced stress responses assisting in the safety assessment of chemicals.UBL - phd migration 201

Targeting the Colchicine Binding Site on Tubulin to Overcome Multidrug Resistance and Anticancer Efficacy of Selective Survivin Inhibitors

Tubulin inhibitors are widely used as chemotherapeutic agents, and their successis attributed to their ability to target microtubule dynamics and disrupt critical cellular functions including cell signaling, motility, intracellular trafficking, and mitosis. Interference with microtubule dynamics consequently disrupts mitotic progression and ultimately leads to apoptosis, validating microtubule dynamics as an excellent target for anticancer agents. While this class of drug has proven to be effective against many cancer types, the clinical efficacy of current tubulin inhibitors is often limited by the development of multidrug resistance. The most common form of resistance to these agents arises from the overexpression of drug efflux transporters. Extensive research efforts have attempted to develop colchicine binding site inhibitors, which are reported to be significantly less susceptible to multidrug resistance and have therapeutic advantages over agents that target the taxane and vinca alkaloid site. Herein, we evaluated the anticancer activity of novel small-molecules that target the colchicine binding site, focusing on the most promising compounds from several structural scaffolds including indolyl-imidazopyridines (DJ95 and DJ101), VERU-111 analogs with a modified indole moiety (10ab and 10bb) or 3,4,5-trimethoxyphenyl moiety (13f), and heterocyclic pyrimidines (4a, 6a, 5a, and 5b). We demonstrated the cytotoxic potency of these compounds against a variety of cancer cell lines, including malignant melanomas, taxaneresistant prostate cancer cells, and drug efflux pump-overexpressing cell lines. Their mechanism of action was revealed through tubulin polymerization inhibition, disruption of microtubule networks and mitotic spindle formation, and confirmed through X-ray crystallography, which detailed their specific molecular interactions with tubulin in the colchicine binding pocket. Furthermore, these compounds exhibited hallmark characteristics of colchicine binding site agents, such as arresting cells in the G2/M phase of the cell cycle, inducing apoptosis in a concentration-dependent manner, and impeding cancer cell proliferation and migration. Finally, the compounds were efficacious in vivo against melanoma and taxane-resistant prostate cancer xenograft tumors. Several agents were evaluated for ability to prevent melanoma metastases to the lungs in experimental mouse models, and they potently inhibited the development metastatic foci. Safety assessment by pharmacological profiling demonstrated minimal interactions to physiologically important targets and pathophysiological analysis of major organs from the in vivo treatment groups did not expose apparent drug-related injury. Several of the investigated compounds also demonstrated vascular disrupting properties by targeting tumor vasculature and inhibiting capillary-like network formation of endothelial cells. Ultimately, these compounds exhibit strong anticancer efficacy, specifically target the colchicine binding site, and have great potential as cancer therapeutics, particularly for multidrug resistance phenotypes. Another target we explored for anticancer intervention was survivin. Survivin is the smallest member the inhibitor of apoptosis protein family and its overexpression in tumor cells is been positively correlated with the development of multidrug resistance and radiation resistance. Because it is differentially expressed in healthy tissues and tumors, it is an attractive therapeutic target. Using the scaffold of UC-112, which was previously identified through virtual screening, we evaluated a series of analogs designed to optimize potency and improve selectivity to survivin over other inhibitor of apoptosis proteins. We identified compound 10f, which was highly cytotoxic to melanoma and Pglycoprotein overexpressing cell lines, induced apoptotic cascades in a concentrationdependent manner, specifically downregulated survivin protein levels, and significantly inhibited tumor growth in vivo. Ultimately, these results validated our in-depth biological investigation of novel scaffolds of survivin inhibitors and verified the anticancer efficacy of 10f

Translational Oncogenomics and Human Cancer Interactome Networks

An overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications of such results are individualized human cancer therapies or, in general, ‘personalized medicine’. Several cancer detection techniques are currently under development both in the direction of improved detection sensitivity and increased time resolution of cellular events, with the limits of single molecule detection and picosecond time resolution already reached. The urgency for the complete mapping of a human cancer interactome with the help of such novel, high-efficiency / low-cost and ultra-sensitive techniques is also pointed out

Screening Approaches for Targeting Ribonucleoprotein Complexes: A New Dimension for Drug Discovery.

RNA-binding proteins (RBPs) are pleiotropic factors that control the processing and functional compartmentalization of transcripts by binding primarily to mRNA untranslated regions (UTRs). The competitive and/or cooperative interplay between RBPs and an array of coding and noncoding RNAs (ncRNAs) determines the posttranscriptional control of gene expression, influencing protein production. Recently, a variety of well-recognized and noncanonical RBP domains have been revealed by modern system-wide analyses, underlying an evolving classification of ribonucleoproteins (RNPs) and their importance in governing physiological RNA metabolism. The possibility of targeting selected RNA-protein interactions with small molecules is now expanding the concept of protein "druggability," with new implications for medicinal chemistry and for a deeper characterization of the mechanism of action of bioactive compounds. Here, taking SF3B1, HuR, LIN28, and Musashi proteins as paradigmatic case studies, we review the strategies applied for targeting RBPs, with emphasis on the technological advancements to study protein-RNA interactions and on the requirements of appropriate validation strategies to parallel high-throughput screening (HTS) efforts

NF-κB Signaling in Macrophages: Dynamics, Crosstalk, and Signal Integration

The nuclear factor-κB (NF-κB) signaling pathway is one of the best understood immune-related pathways thanks to almost four decades of intense research. NF-κB signaling is activated by numerous discrete stimuli and is a master regulator of the inflammatory response to pathogens and cancerous cells, as well as a key regulator of autoimmune diseases. In this regard, the role of NF-κB signaling in immunity is not unlike that of the macrophage. The dynamics by which NF-κB proteins shuttle between the cytoplasm and the nucleus to initiate transcription have been studied rigorously in fibroblasts and other non-hematopoietic cells, but many questions remain as to how current models of NF-κB signaling and dynamics can be translated to innate immune cells such as macrophages. In this review, we will present recent research on the dynamics of NF-κB signaling and focus especially on how these dynamics vary in different cell types, while discussing why these characteristics may be important. We will end by looking ahead to how new techniques and technologies should allow us to analyze these signaling processes with greater clarity, bringing us closer to a more complete understanding of inflammatory transcription factor dynamics and how different cellular contexts might allow for appropriate control of innate immune responses