Cell-to-cell variability in cell death: can systems biology help us make sense of it all?

A morphology and secretome map of pyroptosis

Pyroptosis represents one type of programmed cell death. It is a form of inflammatory cell death that is canonically defined by caspase-1 cleavage and Gasdermin-mediated membrane pore formation. Caspase-1 initiates the inflammatory response (through IL-1β processing), and the N-terminal cleaved fragment of Gasdermin D polymerizes at the cell periphery forming pores to secrete proinflammatory markers. Cell morphology also changes in pyroptosis, with nuclear condensation and membrane rupture. However, recent research challenges canon, revealing a more complex secretome and morphological response in pyroptosis, including overlapping molecular characterization with other forms of cell death, such as apoptosis. Here, we take a multimodal, systems biology approach to characterize pyroptosis. We treated human peripheral blood mononuclear cells (PBMCs) with 36 different combinations of stimuli to induce pyroptosis or apoptosis. We applied both secretome profiling (nELISA) and high-content fluorescence microscopy (Cell Painting). To differentiate apoptotic, pyroptotic, and control cells, we used canonical secretome markers and modified our Cell Painting assay to mark the N-terminus of Gasdermin D. We trained hundreds of machine learning (ML) models to reveal intricate morphology signatures of pyroptosis that implicate changes across many different organelles and predict levels of many proinflammatory markers. Overall, our analysis provides a detailed map of pyroptosis which includes overlapping and distinct connections with apoptosis revealed through a mechanistic link between cell morphology and cell secretome.

Cellular heterogeneity in TNF/TNFR1 signalling: live cell imaging of cell fate decisions in single cells

Cellular responses to TNF are inherently heterogeneous within an isogenic cell population and across different cell types. TNF promotes cell survival by activating pro-inflammatory NF-κB and MAPK signalling pathways but may also trigger apoptosis and necroptosis. Following TNF stimulation, the fate of individual cells is governed by the balance of pro-survival and pro-apoptotic signalling pathways. To elucidate the molecular mechanisms driving heterogenous responses to TNF, quantifying TNF/TNFR1 signalling at the single-cell level is crucial. Fluorescence live-cell imaging techniques offer real-time, dynamic insights into molecular processes in single cells, allowing for detection of rapid and transient changes, as well as identification of subpopulations, that are likely to be missed with traditional endpoint assays. Whilst fluorescence live-cell imaging has been employed extensively to investigate TNF-induced inflammation and TNF-induced cell death, it has been underutilised in studying the role of TNF/TNFR1 signalling pathway crosstalk in guiding cell-fate decisions in single cells. Here, we outline the various opportunities for pathway crosstalk during TNF/TNFR1 signalling and how these interactions may govern heterogenous responses to TNF. We also advocate for the use of live-cell imaging techniques to elucidate the molecular processes driving cell-to-cell variability in single cells. Understanding and overcoming cellular heterogeneity in response to TNF and modulators of the TNF/TNFR1 signalling pathway could lead to the development of targeted therapies for various diseases associated with aberrant TNF/TNFR1 signalling, such as rheumatoid arthritis, metabolic syndrome, and cancer.

Hsp70-Bim incoherent feedforward loop contributes to cell-fate heterogeneity and fractional killing

BACKGROUND AND PURPOSE

Although chemotherapeutics or molecular targeted drugs often elicit profound initial responses, fractional killing capable of driving acquired resistance can persist. Identifying stress-induced negative feedback or an incoherent feedforward loop (IFFL), which may contribute to fractional killing, is urgently needed.

EXPERIMENTAL APPROACH

Mathematical modelling was used to identify how and to what extent a recently reported Hsp70-Bim protein-protein interaction (PPI) contributes to the adaptation of the Bcl-2 network. Experimental validation was made by using a specific inhibitor of Hsp70-Bim PPI, S1g-2, as chemical tool. Bifurcation analysis and stochastic simulation were used for the theoretical study of the impact of Hsp70-Bim PPI on cell-fate heterogeneity and factional killing.

KEY RESULTS

The Hsp70-Bim-AKT circuit forms an IFFL that greatly contributes to the adaptation of the Bcl-2-regulated apoptosis network, thus leading to fractional killing. This adaptive programme enhances noise-induced cell-fate heterogeneity by shifting from a saddle-node to a saddle-collision transition scenario.

CONCLUSION AND IMPLICATIONS

Hsp70-Bim IFFL serves as a molecular pathway induced by DNA damaging drugs or tyrosine kinase inhibitors that enabled fractional killing, whereby acquired resistance emerges. A synergistic strategy is unveiled for overcoming fractional killing by suppressing Hsp70-Bim PPI.

Modulating the dynamics of NFκB and PI3K enhances the ensemble-level TNFR1 signaling mediated apoptotic response

Cell-to-cell variability during TNFα stimulated Tumor Necrosis Factor Receptor 1 (TNFR1) signaling can lead to single-cell level pro-survival and apoptotic responses. This variability stems from the heterogeneity in signal flow through intracellular signaling entities that regulate the balance between these two phenotypes. Using systematic Boolean dynamic modeling of a TNFR1 signaling network, we demonstrate that the signal flow path variability can be modulated to enable cells favour apoptosis. We developed a computationally efficient approach "Boolean Modeling based Prediction of Steady-state probability of Phenotype Reachability (BM-ProSPR)" to accurately predict the network's ability to settle into different phenotypes. Model analysis juxtaposed with the experimental observations revealed that NFκB and PI3K transient responses guide the XIAP behaviour to coordinate the crucial dynamic cross-talk between the pro-survival and apoptotic arms at the single-cell level. Model predicted the experimental observations that ~31% apoptosis increase can be achieved by arresting Comp1 - IKK* activity which regulates the NFκB and PI3K dynamics. Arresting Comp1 - IKK* activity causes signal flow path re-wiring towards apoptosis without significantly compromising NFκB levels, which govern adequate cell survival. Priming an ensemble of cancerous cells with inhibitors targeting the specific interaction involving Comp1 and IKK* prior to TNFα exposure could enable driving them towards apoptosis.

Variability of fluorescence intensity distribution measured by flow cytometry is influenced by cell size and cell cycle progression

The distribution of fluorescence signals measured with flow cytometry can be influenced by several factors, including qualitative and quantitative properties of the used fluorochromes, optical properties of the detection system, as well as the variability within the analyzed cell population itself. Most of the single cell samples prepared from in vitrocultures or clinical specimens contain a variable cell cycle component. Cell cycle, together with changes in the cell size, are two of the factors that alter the functional properties of analyzed cells and thus affect the interpretation of obtained results. Here, we describe the association between cell cycle status and cell size, and the variability in the distribution of fluorescence intensity as determined with flow cytometry, at population scale. We show that variability in the distribution of background and specific fluorescence signals is related to the cell cycle state of the selected population, with the 10% low fluorescence signal fraction enriched mainly in cells in their G0/G1 cell cycle phase, and the 10% high fraction containing cells mostly in the G2/M phase. Therefore we advise using caution and additional experimental validation when comparing populations defined by fractions at both ends of fluorescence signal distribution to avoid biases caused by the effect of cell cycle and cell size.

Next-Generation Personalized Medicine: Implementation of Variability Patterns for Overcoming Drug Resistance in Chronic Diseases

Chronic diseases are a significant healthcare problem. Partial or complete non-responsiveness to chronic therapies is a significant obstacle to maintaining the long-term effect of drugs in these patients. A high degree of intra- and inter-patient variability defines pharmacodynamics, drug metabolism, and medication response. This variability is associated with partial or complete loss of drug effectiveness. Regular drug dosing schedules do not comply with physiological variability and contribute to resistance to chronic therapies. In this review, we describe a three-phase platform for overcoming drug resistance: introducing irregularity for improving drug response; establishing a deep learning, closed-loop algorithm for generating a personalized pattern of irregularity for overcoming drug resistance; and upscaling the algorithm by implementing quantified personal variability patterns along with other individualized genetic and proteomic-based ways. The closed-loop, dynamic, subject-tailored variability-based machinery can improve the efficacy of existing therapies in patients with chronic diseases.

Techniques for studying membrane pores

Pore-forming proteins (PFPs) are of special interest because of the association of their activity with the disruption of the membrane impermeability barrier and cell death. They generally convert from a monomeric, soluble form into transmembrane oligomers that induce the opening of membrane pores. The study of pore formation in membranes with molecular detail remains a challenging endeavor because of its highly dynamic and complex nature, usually involving diverse oligomeric structures with different functionalities. Here we discuss current methods applied for the structural and functional characterization of PFPs at the individual vesicle and cell level. We highlight how the development of high-resolution and single-molecule imaging techniques allows the analysis of the structural organization of protein oligomers and pore entities in lipid membranes.

Ultrasensitive Detection of Enzymatic Activity Using Single Molecule Arrays

Enzyme assays are important for many applications including clinical diagnostics, functional proteomics, and drug discovery. Current methods for enzymatic activity measurement often suffer from low analytical sensitivity. We developed an ultrasensitive method for the detection of enzymatic activity using Single Molecule Arrays (eSimoa). The eSimoa assay is accomplished by conjugating substrates to paramagnetic beads and measuring the conversion of substrates to products using single molecule analysis. We demonstrated the eSimoa method for the detection of protein kinases, telomerase, histone H3 methyltransferase SET7/9, and polypeptide N-acetylgalactosaminyltransferase with unprecedented sensitivity. In addition, we tested enzyme inhibition and performed theoretical calculations for the binding of inhibitor to its target enzyme and show the need for an ultrasensitive enzymatic assay to evaluate the potency of tight binding inhibitors. The eSimoa assay was successfully used to determine inhibition constants of both bosutinib and dasatinib. Due to the ultrasensitivity of this method, we also were able to measure the kinase activities at the single cell level. We show that the eSimoa assay is a simple, fast, and highly sensitive approach, which can be easily extended to detect a variety of other enzymes, providing a promising platform for enzyme-related fundamental research and inhibitor screening.

Variability in microbial inactivation: From deterministic Bigelow model to probability distribution of single cell inactivation times

Phenotypic heterogeneity seems to be an important component leading to biological individuality and is of great importance in the case of microbial inactivation. Bacterial cells are characterized by their own resistance to stresses. This inherent stochasticity is reflected in microbial survival curve which, in this context, can be considered as cumulative probability distribution of lethal events. The objective of the present study was to present an overview on the assessment and quantification of variability in microbial inactivation originating from single cells and discuss this heterogeneity in the context of predicting microbial behavior and Risk assessment studies. The detailed knowledge of the distribution of the single cells' inactivation times can be the basis for stochastic inactivation models which, in turn, may be employed in a risk - based food safety approach.

Glioblastoma Multiforme Stem Cell Cycle Arrest by Alkylaminophenol Through the Modulation of EGFR and CSC Signaling Pathways

Cancer stem cells (CSCs), a small subpopulation of cells existing in the tumor microenvironment promoting cell proliferation and growth. Targeting the stemness of the CSC population would offer a vital therapeutic opportunity. 3,4-Dihydroquinolin-1(2H)-yl)(p-tolyl)methyl)phenol (THTMP), a small synthetic phenol compound, is proposed to play a significant role in controlling the CSC proliferation and survival. We assessed the potential therapeutic effects of THTMP on glioblastoma multiforme (GBM) and its underlying mechanism in various signaling pathways. To fully comprehend the effect of THTMP on the CSCs, CD133⁺ GBM stem cell (GSC) and CD133^- GBM Non-stem cancer cells (NSCC) population from LN229 and SNB19 cell lines was used. Cell cycle arrest, apoptosis assay and transcriptome analysis were performed for individual cell population. THTMP strongly inhibited NSCC and in a subtle way for GSC in a time-dependent manner and inhibit the resistance variants better than that of temozolomide (TMZ). THTMP arrest the CSC cell population at both G1/S and G2/M phase and induce ROS-mediated apoptosis. Gene expression profiling characterize THTMP as an inhibitor of the p53 signaling pathway causing DNA damage and cell cycle arrest in CSC population. We show that the THTMP majorly affects the EGFR and CSC signaling pathways. Specifically, modulation of key genes involved in Wnt, Notch and Hedgehog, revealed the significant role of THTMP in disrupting the CSCs’ stemness and functions. Moreover, THTMP inhibited cell growth, proliferation and metastasis of multiple mesenchymal patient-tissue derived GBM-cell lines. THTMP arrests GBM stem cell cycle through the modulation of EGFR and CSC signaling pathways.

A System for Analog Control of Cell Culture Dynamics to Reveal Capabilities of Signaling Networks

Cellular microenvironments are dynamic. When exposed to extracellular cues, such as changing concentrations of inflammatory cytokines, cells activate signaling networks that mediate fate decisions. Exploring responses broadly to time-varying microenvironments is essential to understand the information transmission capabilities of signaling networks and how dynamic milieus influence cell fate decisions. Here, we present a gravity-driven cell culture and demonstrate that the system accurately produces user-defined concentration profiles for one or more dynamic stimuli. As proof of principle, we monitor nuclear factor-κB activation in single cells exposed to dynamic cytokine stimulation and reveal context-dependent sensitivity and uncharacterized single-cell response classes distinct from persistent stimulation. Using computational modeling, we find that cell-to-cell variability in feedback rates within the signaling network contributes to different response classes. Models are validated using inhibitors to predictably modulate response classes in live cells exposed to dynamic stimuli. These hidden capabilities, uncovered through dynamic stimulation, provide opportunities to discover and manipulate signaling mechanisms.

Physical properties, ligand substitution reactions, and biological activity of Co(iii)-Schiff base complexes

Four cobalt(iii) complexes of the general formula [Co(Schiff base)(L)2]+, where L is ammonia (NH3) or 3-fluorobenzylamine (3F-BnNH2), were synthesized. The complexes were characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography. Their electrochemical properties, ligand substitution mechanisms, and ligand exchange rates in aqueous buffer were investigated. These physical properties were correlated to the cellular uptake and anticancer activities of the complexes. The complexes undergo sequential, dissociative ligand substitution, with the exchange rates depending heavily on the axial ligands. Eyring analyses revealed that the relative ligand exchange rates were largely impacted by differences in the entropy, rather than enthalpy, of activation for the complexes. Performing the substitution reactions in the presence of ascorbate led to a change in the reaction profile and kinetics, but no change in the final product. The cytotoxic activity of the complexes correlates with both the ligand exchange rate and reduction potential, with the more easily reduced and rapidly substituted complexes showing higher toxicity. These relationships may be valuable for the rational design of Co(iii) complexes as anticancer or antiviral prodrugs.

Chlamydia trachomatis fails to protect its growth niche against pro-apoptotic insults

Chlamydia trachomatis is an obligate intracellular bacterial agent responsible for ocular infections and sexually transmitted diseases. It has been postulated that Chlamydia inhibits apoptosis in host cells to maintain an intact replicative niche until sufficient infectious progeny can be generated. Here we report that, while cells infected with C. trachomatis are protected from apoptosis at early and mid-stages of infection, they remain susceptible to the induction of other cell death modalities. By monitoring the fate of infected cells by time-lapse video microscopy and by analyzing host plasma membrane integrity and the activity of caspases, we determined that C. trachomatis-infected cells exposed to pro-apoptotic stimuli predominately died by a mechanism resembling necrosis. This necrotic death of infected cells occurred with kinetics similar to the induction of apoptosis in uninfected cells, indicating that C. trachomatis fails to considerably prolong the lifespan of its host cell when exposed to pro-apoptotic insults. Inhibitors of bacterial protein synthesis partially blocked necrotic death of infected cells, suggesting that the switch from apoptosis to necrosis relies on an active contribution of the bacteria. Tumor necrosis factor alpha (TNF-α)-mediated induction of necrosis in cells infected with C. trachomatis was not dependent on canonical regulators of necroptosis, such as RIPK1, RIPK3, or MLKL, yet was blocked by inhibition or depletion of CASP8. These results suggest that alternative signaling pathways regulate necrotic death in the context of C. trachomatis infections. Finally, consistent with the inability of C. trachomatis to preserve host cell viability, necrosis resulting from pro-apoptotic conditions significantly impaired production of infectious progeny. Taken together, our findings suggest that Chlamydia’s anti-apoptotic activities are not sufficient to protect the pathogen’s replicative niche.

High Throughput Screen Identifies Interferon γ-Dependent Inhibitors of Toxoplasma gondii Growth

Toxoplasma gondii is an obligate intracellular parasite capable of causing severe disease due to congenital infection and in patients with compromised immune systems. Control of infection is dependent on a robust Th1 type immune response including production of interferon gamma (IFN-γ), which is essential for control. IFN-γ activates a variety of antimicrobial mechanisms in host cells, which are then able to control intracellular parasites such as T. gondii. Despite the effectiveness of these pathways in controlling acute infection, the immune system is unable to eradicate chronic infections that can persist for life. Similarly, while antibiotic treatment can control acute infection, it is unable to eliminate chronic infection. To identify compounds that would act synergistically with IFN-γ, we performed a high-throughput screen of diverse small molecule libraries to identify inhibitors of T. gondii. We identified a number of compounds that inhibited parasite growth in vitro at low μM concentrations and that demonstrated enhanced potency in the presence of a low level of IFN-γ. A subset of these compounds act by enhancing the recruitment of light chain 3 (LC3) to the parasite-containing vacuole, suggesting they work by an autophagy-related process, while others were independent of this pathway. The pattern of IFN-γ dependence was shared among the majority of analogs from 6 priority scaffolds, and analysis of structure activity relationships for one such class revealed specific stereochemistry associated with this feature. Identification of these IFN-γ-dependent leads may lead to development of improved therapeutics due to their synergistic interactions with immune responses.

Quantitative single cell analysis uncovers the life/death decision in CD95 network

CD95/Fas/APO-1 is a member of the death receptor family that triggers apoptotic and anti-apoptotic responses in particular, NF-κB. These responses are characterized by a strong heterogeneity within a population of cells. To determine how the cell decides between life and death we developed a computational model supported by imaging flow cytometry analysis of CD95 signaling. Here we show that CD95 stimulation leads to the induction of caspase and NF-κB pathways simultaneously in one cell. The related life/death decision strictly depends on cell-to-cell variability in the formation of the death-inducing complex (DISC) on one side (extrinsic noise) vs. stochastic gene expression of the NF-κB pathway on the other side (intrinsic noise). Moreover, our analysis has uncovered that the stochasticity in apoptosis and NF-kB pathways leads not only to survival or death of a cell, but also causes a third type of response to CD95 stimulation that we termed ambivalent response. Cells in the ambivalent state can undergo cell death or survive which was subsequently validated by experiments. Taken together, we have uncovered how these two competing pathways control the fate of a cell, which in turn plays an important role for development of anti-cancer therapies.

Activation of death receptor (DR) family has been reported to activate both apoptotic as well as anti-apoptotic responses. Molecular mechanisms underlying the intricate details of this crosstalk have not been established yet. Here we show that these pathways are triggered simultaneously in one cell. Furthermore, using stochastic computational modeling we uncovered how an individual cell undergoes apoptosis, while other cells survive upon the same DR activation conditions. This was only possible by combination of computational modeling supported by experimental validation based on the state of the art single cell analysis. The latter included cutting edge technology of imaging flow cytometry, which combines microscopy and flow cytometry in one measurement circuit enabling quantitative analysis of endogenous cellular protein levels estimated from a large number of cells simultaneously. This allowed to shed the light on the question how a single cell possibly avoids apoptosis, which is a highly actual topic in the field of cancer research and development of efficient anti-cancer therapies.

The impact of non-genetic heterogeneity on cancer cell death

The goal of cancer chemotherapy is to induce homogeneous cell death within the population of targeted cancer cells. However, no two cells are exactly alike at the molecular level, and sensitivity to drug-induced cell death, therefore, varies within a population. Genetic alterations can contribute to this variability and lead to selection for drug resistant clones. However, there is a growing appreciation for the role of non-genetic variation in producing drug-tolerant cellular states that exhibit reduced sensitivity to cell death for extended periods of time, from hours to weeks. These cellular states may result from individual variation in epigenetics, gene expression, metabolism, and other processes that impact drug mechanism of action or the execution of cell death. Such population-level non-genetic heterogeneity may contribute to treatment failure and provide a cellular "substrate" for the emergence of genetic alterations that confer frank drug resistance.

Linking nanomaterial properties to biological outcomes: analytical chemistry challenges in nanotoxicology for the next decade

This article provides our perspective on the analytical challenges in nanotoxicology as the field is entering its third decade.

In vitro characterization of alkylaminophenols-induced cell death

Alkylaminophenols are synthetic derivatives well known for their anticancer activity. In the previous studies, we described the activity of the series of Alkylaminophenols derivatives and their ability to induce cell death for many cancer cell lines. However, temporal heterogeneity in cell death induced by lead compounds, N-(2-hydroxy-5-nitrophenyl (4'-methylphenyl) methyl) indoline (Compound I) and 2-((3,4-dihydroquinolin-1(2H)-yl) (4-methoxyphenyl) methyl) phenol (Compound II), has never been tested on osteosarcoma cells (U2OS). Here, we address the level of cell-to-cell heterogeneity by examine whether differences in the type of compounds could influence its effects on cell death of U2OS. Here, we applied imaging, computational methods and biochemical methods to study heterogeneity, apoptosis, reactive oxygen species and caspase. Our results demonstrate that the Hill coefficient of dose-response curve of Compound II is greater than compound I in treated U2OS cells. Both Compounds trigger not only apoptotic cell death but also necro-apoptotic and necrotic cell death. The percentage of these sub-populations varies depending on compounds in which greater variance is induced by compound II than Compound I. We also identified the accumulation of compounds-induced reactive oxygen species during the treatment. This resulted in caspase 3/7 activation in turn induced apoptosis. In summary, the screening of Compound I and II molecules for heterogeneity, apoptosis, reactive oxygen species and caspase has identified compound II as promising anti-osteosarcoma cancer agent. Compound II could be a promising lead compound for future antitumor agent development.

Bis(thiosemicarbazone) Complexes of Cobalt(III). Synthesis, Characterization, and Anticancer Potential

Nine bis(thiosemicarbazone) (BTSC) cobalt(III) complexes of the general formula [Co(BTSC)(L)2]NO3 were synthesized, where BTSC = diacetyl bis(thiosemicarbazone) (ATS), pyruvaldehyde bis(thiosemicarbazone) (PTS), or glyoxal bis(thiosemicarbazone) (GTS) and L = ammonia, imidazole (Im), or benzylamine (BnA). These compounds were characterized by multinuclear NMR spectroscopy, mass spectrometry, cyclic voltammetry, and X-ray crystallography. Their stability in phosphate-buffered saline was investigated and found to be highly dependent on the nature of the axial ligand, L. These studies revealed that complex stability is primarily dictated by the axial ligand following the sequence NH3 > Im > BnA. The cellular uptake and cytotoxicity in cancer cells were also determined. Both the cellular uptake and cytotoxicity were significantly affected by the nature of the equatorial BTSC. Complexes of ATS were taken up much more effectively than those of PTS and GTS. The cytotoxicity of the complexes was correlated to that of the free ligand. Cell uptake and cytotoxicity were also determined under hypoxic conditions. Only minor differences in the hypoxia activity and uptake were observed. Treatment of the cancer cells with the copper-depleting agent tetrathiomolybdate decreased the cytotoxic potency of the complexes, indicating that they may operate via a copper-dependent mechanism. These results provide a structure-activity relationship for this class of compounds, which may be applied for the rational design of new cobalt(III) anticancer agents.

Computer modeling of ischemic stroke

The occlusion of a blood vessel in the brain causes an ischemic stroke. Current treatment relies restoration of blood flow within 3 hours. Substantial research has focused on neuroprotection to spare compromised neural tissue and extend the treatment time window. Despite success with animal models and extensive associated clinical testing, there are still no therapies of this kind. Ischemic stroke is fundamentally a multiscale phenomenon where a cascade of changes triggered by loss of blood flow involves processes at spatial scales from molecular to centimeters with damage occurring in milliseconds to days and recovery into years. Multiscale computational modeling is a technique to assist understanding of the many agents involved in these multitudinous interacting pathways to provide clues for in silico development of multi-target polypharmacy drug cocktails.

Using Pharmacogenomic Databases for Discovering Patient-Target Genes and Small Molecule Candidates to Cancer Therapy

With multiple omics strategies being applied to several cancer genomics projects, researchers have the opportunity to develop a rational planning of targeted cancer therapy. The investigation of such numerous and diverse pharmacogenomic datasets is a complex task. It requires biological knowledge and skills on a set of tools to accurately predict signaling network and clinical outcomes. Herein, we describe Web-based in silico approaches user friendly for exploring integrative studies on cancer biology and pharmacogenomics. We briefly explain how to submit a query to cancer genome databases to predict which genes are significantly altered across several types of cancers using CBioPortal. Moreover, we describe how to identify clinically available drugs and potential small molecules for gene targeting using CellMiner. We also show how to generate a gene signature and compare gene expression profiles to investigate the complex biology behind drug response using Connectivity Map. Furthermore, we discuss on-going challenges, limitations and new directions to integrate molecular, biological and epidemiological information from oncogenomics platforms to create hypothesis-driven projects. Finally, we discuss the use of Patient-Derived Xenografts models (PDXs) for drug profiling in vivo assay. These platforms and approaches are a rational way to predict patient-targeted therapy response and to develop clinically relevant small molecules drugs.

IRES inhibition induces terminal differentiation and synchronized death in triple-negative breast cancer and glioblastoma cells

Internal ribosome entry site (IRES)-mediated translation is a specialized mode of protein synthesis which malignant cells depend on to survive adverse microenvironmental conditions. Our lab recently reported the identification of a group of compounds which selectively interfere with IRES-mediated translation, completely blocking de novo IGF1R synthesis, and differentially modulating synthesis of the two c-Myc isoforms. Here, we examine the phenotypic consequences of sustained IRES inhibition in human triple-negative breast carcinoma and glioblastoma cells. A sudden loss of viability affects the entire tumor cell population after ∼72-h continuous exposure to the lead compound. The extraordinarily steep dose-response relationship (Hill-Slope coefficients −15 to −35) and extensive physical connections established between the cells indicate that the cells respond to IRES inhibition collectively as a population rather than as individual cells. Prior to death, the treated cells exhibit prominent features of terminal differentiation, with marked gains in cytoskeletal organization, planar polarity, and formation of tight junctions or neuronal processes. In addition to IGF1R and Myc, specific changes in connexin 43, BiP, CHOP, p21, and p27 also correlate with phenotypic outcome. This unusual mode of tumor cell death is absolutely dependent on exceeding a critical threshold in cell density, suggesting that a quorum-sensing mechanism may be operative. Death of putative tumor stem cells visualized in situ helps to explain the inability of tumor cells to recover and repopulate once the compound is removed. Together, these findings support the concept that IRES-mediated translation is of fundamental importance to maintenance of the undifferentiated phenotype and survival of undifferentiated malignant cells.

Time-Resolved Study of Nanoparticle Induced Apoptosis Using Microfabricated Single Cell Arrays

Cell fate decisions like apoptosis are heterogeneously implemented within a cell population and, consequently, the population response is recognized as sum of many individual dynamic events. Here, we report on the use of micro-patterned single-cell arrays for real-time tracking of nanoparticle-induced (NP) cell death in sets of thousands of cells in parallel. Annexin (pSIVA) and propidium iodide (PI), two fluorescent indicators of apoptosis, are simultaneously monitored after exposure to functionalized polystyrene (PS - NH 2) nanobeads as a model system. We find that the distribution of Annexin onset times shifts to later times and broadens as a function of decreasing NP dose. We discuss the mean time-to-death as a function of dose, and show how the EC 50 value depends both on dose and time of measurement. In addition, the correlations between the early and late apoptotic markers indicate a systematic shift from apoptotic towards necrotic cell death during the course of the experiment. Thus, our work demonstrates the potential of array-based single cell cytometry for kinetic analysis of signaling cascades in a high-throughput format.

Bax assembly into rings and arcs in apoptotic mitochondria is linked to membrane pores

Bax is a key regulator of apoptosis that, under cell stress, accumulates at mitochondria, where it oligomerizes to mediate the permeabilization of the mitochondrial outer membrane leading to cytochrome c release and cell death. However, the underlying mechanism behind Bax function remains poorly understood. Here, we studied the spatial organization of Bax in apoptotic cells using dual-color single-molecule localization-based super-resolution microscopy. We show that active Bax clustered into a broad distribution of distinct architectures, including full rings, as well as linear and arc-shaped oligomeric assemblies that localized in discrete foci along mitochondria. Remarkably, both rings and arcs assemblies of Bax perforated the membrane, as revealed by atomic force microscopy in lipid bilayers. Our data identify the supramolecular organization of Bax during apoptosis and support a molecular mechanism in which Bax fully or partially delineates pores of different sizes to permeabilize the mitochondrial outer membrane.

Lifetime Distributions from Tracking Individual BC3H1 Cells Subjected to Yessotoxin

This work shows examples of lifetime distributions for individual BC3H1 cells after start of exposure to the marine toxin yessotoxin (YTX) in an experimental dish. The present tracking of many single cells from time-lapse microscopy data demonstrates the complexity in individual cell fate and which can be masked in aggregate properties. This contribution also demonstrates the general practicality of cell tracking. It can serve as a conceptually simple and non-intrusive method for high throughput early analysis of cytotoxic effects to assess early and late time points relevant for further analyzes or to assess for variability and sub-populations of interest. The present examples of lifetime distributions seem partly to reflect different cell death modalities. Differences between cell lifetime distributions derived from populations in different experimental dishes can potentially provide measures of inter-cellular influence. Such outcomes may help to understand tumor-cell resistance to drug therapy and to predict the probability of metastasis.

Surviving apoptosis: life-death signaling in single cells

Tissue development and homeostasis are regulated by opposing pro-survival and pro-death signals. An interesting feature of the Tumor Necrosis Factor (TNF) family of ligands is that they simultaneously activate opposing signals within a single cell via the same ligand-receptor complex. The magnitude of pro-death events such as caspase activation and pro-survival events such as Nuclear Factor (NF)-κB activation vary not only from one cell type to the next but also among individual cells of the same type due to intrinsic and extrinsic noise. The molecules involved in these pro-survival and/or pro-death pathways, and the different phenotypes that result from their activities, have been recently reviewed. Here we focus on the impact of cell-to-cell variability in the strength of these opposing signals on shaping cell fate decisions.

Bioenergetic disruption of human micro-vascular endothelial cells by antipsychotics

Antipsychotics (APs) are widely used medications, however these are not without side effects such as disruption of blood brain barrier function (BBB). To investigate this further we have studied the chronic effects of the typical APs, chlorpromazine (CPZ) and haloperidol (HAL) and the atypical APs, risperidone (RIS) and clozapine (CLZ), on the bioenergetics of human micro-vascular endothelial cells (HBVECs) of the BBB. Alamar blue (AB) and ATP assays showed that these APs impair bioenergenesis in HBVECs in a concentration and time dependent manner. However since these effects were incomplete they suggest a population of cell bioenergetically heterogeneous, an idea supported by the bistable nature by which APs affected the mitochondrial transmembrane potential. CPZ, HAL and CLZ inhibited the activity of mitochondrial complexes I and III. Our data demonstrates that at therapeutic concentrations, APs can impair the bioenergetic status of HBVECs, an action that help explains the adverse side effects of these drugs when used clinically.

Systems biology of death receptor networks: live and let die

The extrinsic apoptotic pathway is initiated by death receptor activation. Death receptor activation leads to the formation of death receptor signaling platforms, resulting in the demolition of the cell. Despite the fact that death receptor-mediated apoptosis has been studied to a high level of detail, its quantitative regulation until recently has been poorly understood. This situation has dramatically changed in the last years. Creation of mathematical models of death receptor signaling led to an enormous progress in the quantitative understanding of the network regulation and provided fascinating insights into the mechanisms of apoptosis control. In the following sections, the models of the death receptor signaling and their biological implications will be addressed. Central attention will be given to the models of CD95/Fas/APO-1, an exemplified member of the death receptor signaling pathways. The CD95 death-inducing signaling complex (DISC) and regulation of CD95 DISC activity by its key inhibitor c-FLIP, have been vigorously investigated by modeling approaches, and therefore will be the major topic here. Furthermore, the non-linear dynamics of the DISC, positive feedback loops and bistability as well as stoichiometric switches in extrinsic apoptosis will be discussed. Collectively, this review gives a comprehensive view how the mathematical modeling supported by quantitative experimental approaches has provided a new understanding of the death receptor signaling network.