Search

Objective Trained immunity (TI) is a de facto memory program of innate immune cells, characterized by immunometabolic and epigenetic changes sustaining enhanced production of cytokines. TI evolved as a protective mechanism against infections; however, inappropriate activation can cause detrimental inflammation and might be implicated in the pathogenesis of chronic inflammatory diseases. In this study, we investigated the role of TI in the pathogenesis of giant cell arteritis (GCA), a large-vessel vasculitis characterized by aberrant macrophage activation and excess cytokine production. Methods Monocytes from GCA patients and from age- and sex-matched healthy donors were subjected to polyfunctional studies, including cytokine production assays at baseline and following stimulation, intracellular metabolomics, chromatin immunoprecipitation-qPCR, and combined ATAC/RNA sequencing. Immunometabolic activation (i.e. glycolysis) was assessed in inflamed vessels of GCA patients with FDG-PET and immunohistochemistry (IHC), and the role of this pathway in sustaining cytokine production was confirmed with selective pharmacologic inhibition in GCA monocytes. Results GCA monocytes exhibited hallmark molecular features of TI. Specifically, these included enhanced IL-6 production upon stimulation, typical immunometabolic changes (e.g. increased glycolysis and glutaminolysis) and epigenetic changes promoting enhanced transcription of genes governing pro-inflammatory activation. Immunometabolic changes of TI (i.e. glycolysis) were a feature of myelomonocytic cells in GCA lesions and were required for enhanced cytokine production. Conclusions Myelomonocytic cells in GCA activate TI programs sustaining enhanced inflammatory activation with excess cytokine production. [ABSTRACT FROM AUTHOR]

The transcription factor family of nuclear factor kappa B (NF-κB) proteins is widely recognized as a key player in inflammation and the immune responses, where it plays a fundamental role in translating external inflammatory cues into precise transcriptional programs, including the timely expression of a wide variety of cytokines/chemokines. Live cell imaging in single cells showed approximately 15 years ago that the canonical activation of NF-κB upon stimulus is very dynamic, including oscillations of its nuclear localization with a period close to 1.5 hours. This observation has triggered a fruitful interdisciplinary research line that has provided novel insights on the NF-κB system: how its heterogeneous response differs between cell types but also within homogeneous populations; how NF-κB dynamics translate external cues into intracellular signals and how NF-κB dynamics affects gene expression. Here we review the main features of this live cell imaging approach to the study of NF-κB, highlighting the key findings, the existing gaps of knowledge and hinting towards some of the potential future steps of this thriving research field. [ABSTRACT FROM AUTHOR]

Boosting antitumor immunity has emerged as a powerful strategy in cancer treatment. While releasing T‐cell brakes has received most attention, tumor recognition by T cells is a pre‐requisite. Radiotherapy and certain cytotoxic drugs induce the release of damage‐associated molecular patterns, which promote tumor antigen cross‐presentation and T‐cell priming. Antibodies against the "do not eat me" signal CD47 cause macrophage phagocytosis of live tumor cells and drive the emergence of antitumor T cells. Here we show that CXCR4 activation, so far associated only with tumor progression and metastasis, also flags tumor cells to immune recognition. Both CXCL12, the natural CXCR4 ligand, and BoxA, a fragment of HMGB1, promote the release of DAMPs and the internalization of CD47, leading to protective antitumor immunity. We designate as Immunogenic Surrender the process by which CXCR4 turns in tumor cells to macrophages, thereby subjecting a rapidly growing tissue to immunological scrutiny. Importantly, while CXCL12 promotes tumor cell proliferation, BoxA reduces it, and might be exploited for the treatment of malignant mesothelioma and a variety of other tumors. Synopsis: Induction of antitumor immunity is a successful strategy in cancer treatment. This study reports that BoxA, a fragment of the alarmin HMGB1, induces tumor remission and antitumor immunity in mouse models of mesothelioma and colon carcinoma. Both BoxA and the chemokine CXCL12 bind the G‐Protein Coupled Receptor CXCR4.CXCR4 and CD47 are in contact on the surface of tumor cells and co‐internalize upon CXCR4 engagement by either BoxA or CXCL12.Both CXCL12 and BoxA induce the phagocytosis of tumor cells by macrophages.BoxA inhibits tumor cell growth and induces antitumor immunological memory in syngeneic mouse models of mesothelioma or colon carcinoma.CXCL12 is suggested to mediate a similar response (Immunogenic Surrender) in a fraction of untreated tumor‐bearing mice. [ABSTRACT FROM AUTHOR]

The eukaryotic transcriptional regulator Nuclear Factor kappa B (NF-κB) plays a central role in the defense to pathogens. Despite this, few studies have analyzed NF-κB activity in single cells during infection. Here, we investigated at the single cell level how NF-κB nuclear localization – a proxy for NF-κB activity – oscillates in infected and uninfected fibroblasts co-existing in cultures exposed toSalmonella entericaserovar Typhimurium. Fibroblasts were used due to the capacity ofS. Typhimurium to persist in this cell type. Real-time dynamics of NF-κB was examined in microfluidics, which prevents cytokine accumulation. In this condition, infected (ST+) cells translocate NF-κB to the nucleus at higher rate than the uninfected (ST-) cells. Surprisingly, in non-flow (static) culture conditions, ST- fibroblasts exhibited higher NF-κB nuclear translocation than the ST+ population, with these latter cells turning refractory to external stimuli such as TNF-α or a second infection. Sorting of ST+ and ST- cell populations confirmed enhanced expression of NF-κB target genes such asIL1B, NFKBIA, TNFAIP3, andTRAF1in uninfected (ST-) fibroblasts. These observations proved thatS. Typhimurium dampens the NF-κB response in the infected fibroblast. Higher expression ofSOCS3, encoding a “suppressor of cytokine signaling,” was also observed in the ST+ population. IntracellularS. Typhimurium subverts NF-κB activity using protein effectors translocated by the secretion systems encoded by pathogenicity islands 1 (T1) and 2 (T2). T1 is required for regulating expression ofSOCS3and all NF-κB target genes analyzed whereas T2 displayed no role in the control ofSOCS3andIL1Bexpression. Collectively, these data demonstrate thatS. Typhimurium attenuates NF-κB signaling in fibroblasts, an effect only perceptible when ST+ and ST- populations are analyzed separately. This tune-down in a central host defense might be instrumental forS. Typhimurium to establish intracellular persistent infections. [ABSTRACT FROM AUTHOR]

Several transcription factors (TFs) oscillate, periodically relocating between the cytoplasm and the nucleus. NF-κB, which plays key roles in inflammation and cancer, displays oscillations whose biological advantage remains unclear. Recent work indicated that NF-κB displays sustained oscillations that can be entrained, that is, reach a persistent synchronized state through small periodic perturbations. We show here that for our GFP-p65 knock-in cells NF-κB behaves as a damped oscillator able to synchronize to a variety of periodic external perturbations with no memory. We imposed synchronous dynamics to prove that transcription of NF-κB-controlled genes also oscillates, but mature transcript levels follow three distinct patterns. Two sets of transcripts accumulate fast or slowly, respectively. Another set, comprising chemokine and chemokine receptor mRNAs, oscillates and resets at each new stimulus, with no memory of the past. We propose that TF oscillatory dynamics is a means of segmenting time to provide renewing opportunity windows for decision. [ABSTRACT FROM AUTHOR]

Gene expression is an inherently stochastic process that depends on the structure of the biochemical regulatory network in which the gene is embedded. Here we study the dynamical consequences of the interplay between stochastic gene switching and the widespread negative feedback regulatory loop in a simple model of a biochemical regulatory network. Using a simplified hybrid simulation approach, in which only the gene activation is modeled stochastically, we find that stochasticity in gene switching by itself can induce pulses in the system, providing also analytical insights into their origin. Furthermore, we find that this simple network is able to reproduce both exponential and peaked distributions of gene active and inactive times similar to those that have been observed experimentally. This simplified hybrid simulation approach also allows us to link these patterns to the dynamics of the system for each gene state. [ABSTRACT FROM AUTHOR]

Abstract: The mathematical modeling of the oscillations has attracted considerable attention in recent times, but there is a lack of simple models in the literature that can capture the main features of the dynamics of this important transcription factor. For this reason we propose a simple model that summarizes the key steps of the pathway. We show that the resulting 5-dimensional dynamical system can reproduce different phenomena observed in experiments. Our model can display smooth and spiky oscillations in the amount of nuclear and can reproduce the variety of dynamics observed when different stimulations such as and LPS are used. Furthermore we show that the model can be easily extended to reproduce the expression of early, intermediate and late genes upon stimulation. As a final example we show that our simple model can mimic the different transcriptional outputs observed when cells are treated with two different drugs leading to nuclear localization of : Leptomycin B and Cycloheximide. [Copyright &y& Elsevier]

NF-κB is a transcription factor that upon activation undergoes cycles of cytoplasmic-to-nuclear and nuclear-to-cytoplasmic transport, giving rise to so called “oscillations”. In turn, oscillations tune the transcriptional output. Since a detailed understanding of oscillations requires a systems biology approach, we developed a method to acquire and analyze large volumes of data on NF-κB dynamics in single cells. We measured the time evolution of the nuclear to total ratio of GFP-p65 in knock-in mouse embryonic fibroblasts using time-lapse imaging. We automatically produced a precise segmentation of nucleus and cytoplasm based on an accurate estimation of the signal and image background. Finally, we defined a set of quantifiers that describe the oscillatory dynamics, which are internally normalized and can be used to compare data recorded by different labs. Using our method, we analyzed NF-κB dynamics in over 2000 cells exposed to different concentrations of TNF- α α. We reproduced known features of the NF-κB system, such as the heterogeneity of the response in the cell population upon stimulation and we confirmed that a fraction of the responding cells does not oscillate. We also unveiled important features: the second and third oscillatory peaks were often comparable to the first one, a basal amount of nuclear NF-κB could be detected in unstimulated cells, and at any time a small fraction of unstimulated cells showed spontaneous random activation of the NF-κB system. Our work lays the ground for systematic, high-throughput, and unbiased analysis of the dynamics of transcription factors that can shuttle between the nucleus and other cell compartments. [ABSTRACT FROM AUTHOR]

Chaotic scattering in open Hamiltonian systems is relevant for different problems in physics. Particles in such kind of systems can exhibit both bounded or unbounded motions for which escapes from the scattering region can take place. This paper analyzes how to control the escape of the particles from the scattering region in the presence of noise. For that purpose, we apply the partial control technique to the Hénon-Heiles system, which implies that we need to use a control smaller than the noise present in the system. The main finding of our work is the successful control of the particles in the scattering region with a control smaller than noise. We have also analyzed and compared the escapes time of orbits in the scattering region for different situations. Finally, we believe that our results might contribute to a better understanding of both chaotic scattering phenomena and the application of the partial control technique to continuous dynamical systems. [ABSTRACT FROM AUTHOR]

We present an analog circuit implementation of the novel partial control method, that is able to sustain chaotic transient dynamics. The electronic circuit simulates the dynamics of the one-dimensional slope-three tent map, for which the trajectories diverge to infinity for nearly all the initial conditions after behaving chaotically for a while. This is due to the existence of a nonattractive chaotic set: a chaotic saddle. The partial control allows one to keep the trajectories close to the chaotic saddle, even if the control applied is smaller than the effect of the applied noise, introduced into the system. Furthermore, we also show here that similar results can be implemented on a circuit that simulates a horseshoe-like map, which is a simple extension of the previous one. This encouraging result validates the theory and opens new perspectives for the application of this technique to systems with higher dimensions and continuous time dynamics. [ABSTRACT FROM AUTHOR]

In this paper, we study the nonlinear response of the nonlinear mass-spring model with nonsmooth stiffness. For this purpose, we take as prototype model, a system that consists of the double-well smooth potential with an additional spring component acting on the system only for large enough displacement. We focus our study on the analysis of the homoclinic orbits for such nonlinear potential for which we observe the appearance of chaotic motion in the presence of damping effects and an external harmonic force, analyzing the crucial role of the linear spring in the dynamics of our system. The results are shown by using both the Melnikov analysis and numerical simulations. We expect our work to have implications on problems concerning the suspension of vehicles, among others. [ABSTRACT FROM AUTHOR]

We study, both numerically and experimentally, the synchronization of uncoupled excitable systems due to a common noise. We consider two identical FitzHugh-Nagumo systems, which display both spiking and nonspiking behaviours in chaotic or periodic regimes. An electronic circuit provides a laboratory implementation of these dynamics. Synchronization is tested with both white and coloured noise, showing that coloured noise is more effective in inducing synchronization of the systems. We also study the effects on the synchronization of parameter mismatch and of the presence of intrinsic (not common) noise, and we conclude that the best performance of coloured noise is robust under these distortions. [ABSTRACT FROM AUTHOR]

Abstract: This Letter shows that a suitable chaotic signal can induce resonant effects analogous to those observed in presence of noise in a bistable system under periodic forcing. By constructing groups of chaotic and random perturbations with similar one-time statistics we show that in some cases chaos and noise induce indistinguishable resonant effects. This reinforces the conjecture by which in some situations where noise is supposed to play a key role maybe chaos is the key ingredient. Here we also show that the presence of a chaotic signal as the perturbation leading to a resonance opens new control perspectives based on our ability to stabilize chaos in different periodic orbits. A discussion of the possible implications of these facts is also presented at the end of the Letter. [Copyright &y& Elsevier]

A well-known method to suppress chaos in a periodically forced chaotic system is to add a harmonic perturbation. The phase control of chaos scheme uses the phase difference between a small added harmonic perturbation and the main driving to suppress chaos, leading the system to different periodic orbits. Using the Duffing oscillator as a paradigm, we present here an in-depth study of this technique. A thorough numerical exploration has been made focused in the important role played by the phase, from which new interesting patterns in parameter space have appeared. On the other hand, our novel experimental implementation of phase control in an electronic circuit confirms both the well-known features of this method and the new ones detected numerically. All this may help in future implementations of phase control of chaos, which is globally confirmed here to be robust and easy to implement experimentally. [ABSTRACT FROM AUTHOR]

In this review, we aim at describing the results obtained in the past years on dynamics features defining NF-κB regulatory functions, as we believe that these developments might have a transformative effect on the way in which NF-κB involvement in cancer is studied. We will also describe technical aspects of the studies performed in this context, including the use of different cellular models, culture conditions, microscopy approaches and quantification of the imaging data, balancing their strengths and limitations and pointing out to common features and to some open questions. Our emphasis in the methodology will allow a critical overview of literature and will show how these cutting-edge approaches can contribute to shed light on the involvement of NF-κB deregulation in tumour onset and progression. We hypothesize that this “dynamic point of view” can be fruitfully applied to untangle the complex relationship between NF-κB and cancer and to find new targets to restrain cancer growth. [ABSTRACT FROM AUTHOR]

Valproic acid (VPA) is an effective and widely used anti-seizure medication but is teratogenic when used during pregnancy, affecting brain and spinal cord development for reasons that remain largely unclear. Here we designed a genetic recombinase-based SOX10 reporter system in human pluripotent stem cells that enables tracking and lineage tracing of Neural Crest cells (NCCs) in a human organoid model of the developing neural tube. We found that VPA induces extensive cellular senescence and promotes mesenchymal differentiation of human NCCs. We next show that the clinically approved drug Rapamycin inhibits senescence and restores aberrant NCC differentiation trajectory after VPA exposure in human organoids and in developing zebrafish, highlighting the therapeutic promise of this approach. Finally, we identify the pioneer factor AP1 as a key element of this process. Collectively our data reveal cellular senescence as a central driver of VPA-associated neurodevelopmental teratogenicity and identifies a new pharmacological strategy for prevention. These results exemplify the power of genetically modified human stem cell-derived organoid models for drug discovery., (© 2024. The Author(s).)

Trained immunity (TI) is a proinflammatory program induced in monocyte/macrophages upon sensing of specific pathogens and is characterized by immunometabolic and epigenetic changes that enhance cytokine production. Maladaptive activation of TI (ie, in the absence of infection) may result in detrimental inflammation and development of disease; however, the exact role and extent of inappropriate activation of TI in the pathogenesis of human diseases is undetermined. In this study, we uncovered the oncogene-induced, maladaptive induction of TI in the pathogenesis of a human inflammatory myeloid neoplasm (Erdheim-Chester disease, [ECD]), characterized by the BRAFV600E oncogenic mutation in monocyte/macrophages and excess cytokine production. Mechanistically, myeloid cells expressing BRAFV600E exhibit all molecular features of TI: activation of the AKT/mammalian target of rapamycin signaling axis; increased glycolysis, glutaminolysis, and cholesterol synthesis; epigenetic changes on promoters of genes encoding cytokines; and enhanced cytokine production leading to hyperinflammatory responses. In patients with ECD, effective therapeutic strategies combat this maladaptive TI phenotype; in addition, pharmacologic inhibition of immunometabolic changes underlying TI (ie, glycolysis) effectively dampens cytokine production by myeloid cells. This study revealed the deleterious potential of inappropriate activation of TI in the pathogenesis of human inflammatory myeloid neoplasms and the opportunity for inhibition of TI in conditions characterized by maladaptive myeloid-driven inflammation., (© 2021 by The American Society of Hematology.)

Nuclear positioning within cells is important for multiple cellular processes in development and regeneration. The most intriguing example of nuclear positioning occurs during skeletal muscle differentiation. Muscle fibers (myofibers) are multinucleated cells formed by the fusion of muscle precursor cells (myoblasts) derived from muscle stem cells (satellite cells) that undergo proliferation and differentiation. Correct nuclear positioning within myofibers is required for the proper muscle regeneration and function. The common procedure to assess myoblast differentiation and myofiber formation relies on fixed cells analyzed by immunofluorescence, which impedes the study of nuclear movement and cell behavior over time. Here, we describe a method for the analysis of myoblast differentiation and myofiber formation by live cell imaging. We provide a software for automated nuclear tracking to obtain a high-throughput quantitative characterization of nuclear dynamics and myoblast behavior (i.e., the trajectory) during differentiation and fusion.

In this paper we make a thorough exploration of the technique of partial control of chaotic systems. This control technique allows one to keep the trajectories of a dynamical system close to a chaotic saddle even if the control applied is smaller than the effects of environmental noise in the system, provided that the chaotic saddle is due to the existence of a horseshoelike mapping in phase space. We state this here in a mathematically precise way using the Conley-Moser conditions, and we prove that they imply that our partial control strategy can be applied. We also give an upper bound of the control-noise ratio needed to achieve this goal, and we describe how this technique can be applied for large noise values. Finally, we study in detail the effect of imperfect targeting in our control technique. All these results are illustrated numerically with the paradigmatic Hénon map.

In this paper we study how to avoid escapes in open dynamical systems in the presence of dissipation and forcing, as it occurs in realistic physical situations. We use as a prototype model the Helmholtz oscillator, which is the simplest nonlinear oscillator with escapes. For some parameter values, this oscillator presents a critical value of the forcing for which all particles escape from its single well. By using the phase control technique, weakly changing the shape of the potential via a periodic perturbation of suitable phase varphi , we avoid the escapes in different regions of the phase space. We provide numerical evidence, heuristic arguments, and an experimental implementation in an electronic circuit of this phenomenon. Finally, we expect that this method might be useful for avoiding escapes in more complicated physical situations.

In a region in phase space where there is a chaotic saddle, all initial conditions will escape from it after a transient with the exception of a set of points of zero Lebesgue measure. The action of an external noise makes all trajectories escape faster. Attempting to avoid those escapes by applying a control smaller than noise seems to be an impossible task. Here we show, however, that this goal is indeed possible, based on a geometrical property found typically in this situation: the existence of a horseshoe. The horseshoe implies that there exist what we call safe sets, which assures that there is a general strategy that allows one to keep trajectories inside that region with control smaller than noise. We call this type of control partial control of chaos.

We present a nonfeedback method to tame or enhance crisis-induced intermittency in dynamical systems. By adding a small harmonic perturbation to a parameter of the system, the intermittent behavior can be suppressed or enhanced depending on the value of the phase difference between the main driving and the perturbation. The validity of the method is shown both in the model and in an experiment with a CO2 laser. An analysis of this scheme applied to the quadratic map near crisis illustrates the role of phase control in nonlinear dynamical systems.