Small transcriptional differences among cell clones lead to distinct NF-κB dynamics

Transcription factor dynamics is fundamental to determine the activation of accurate transcriptional programs and yet is heterogeneous at a single-cell level, even within homogeneous populations. We asked how such heterogeneity emerges for the nuclear factor κB (NF-κB). We found that clonal populations of immortalized fibroblasts derived from a single mouse embryo display robustly distinct NF-κB dynamics upon tumor necrosis factor ɑ (TNF-ɑ) stimulation including persistent, oscillatory, and weak activation, giving rise to differences in the transcription of its targets. By combining transcriptomics and simulations we show how less than two-fold differences in the expression levels of genes coding for key proteins of the signaling cascade and feedback system are predictive of the differences of the NF-κB dynamic response of the clones to TNF-ɑ and IL-1β. We propose that small transcriptional differences in the regulatory circuit of a transcription factor can lead to distinct signaling dynamics in cells within homogeneous cell populations and among different cell types.

Myelomonocytic cells in giant cell arteritis activate trained immunity programs sustaining inflammation and cytokine production

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.

The transcriptional regulator Sin3A balances IL-17A and Foxp3 expression in primary CD4 T cells

The Sin3 transcriptional regulator homolog A (Sin3A) is the core member of a multiprotein chromatin-modifying complex. Its inactivation at the CD4/CD8 double-negative stage halts further thymocyte development. Among various functions, Sin3A regulates STAT3 transcriptional activity, central to the differentiation of Th17 cells active in inflammatory disorders and opportunistic infections. To further investigate the consequences of conditional Sin3A inactivation in more mature precursors and post-thymic T cell, we have generated CD4-Cre and CD4-CreER^T2 Sin3A^F/F mice. Sin3A inactivation in vivo hinders both thymocyte development and peripheral T-cell survival. In vitro, in Th17 skewing conditions, Sin3A-deficient cells proliferate and acquire memory markers and yet fail to properly upregulate Il17a, Il23r, and Il22. Instead, IL-2⁺ and FOXP3⁺ are mostly enriched for, and their inhibition partially rescues IL-17A⁺ T cells. Notably, Sin3A deletion also causes an enrichment of genes implicated in the mTORC1 signaling pathway, overt STAT3 activation, and aberrant cytoplasmic RORγt accumulation. Thus, together our data unveil a previously unappreciated role for Sin3A in shaping critical signaling events central to the acquisition of immunoregulatory T-cell phenotypes.

Nucleosomes effectively shield DNA from radiation damage in living cells

Eukaryotic DNA is organized in nucleosomes, which package DNA and regulate its accessibility to transcription, replication, recombination and repair. Here, we show that in living cells nucleosomes protect DNA from high-energy radiation and reactive oxygen species. We combined sequence-based methods (ATAC-seq and BLISS) to determine the position of both nucleosomes and double strand breaks (DSBs) in the genome of nucleosome-rich malignant mesothelioma cells, and of the same cells partially depleted of nucleosomes. The results were replicated in the human MCF-7 breast carcinoma cell line. We found that, for each genomic sequence, the probability of DSB formation is directly proportional to the fraction of time it is nucleosome-free; DSBs accumulate distal from the nucleosome dyad axis. Nucleosome free regions and promoters of actively transcribed genes are more sensitive to DSB formation, and consequently to mutation. We argue that this may be true for a variety of chemical and physical DNA damaging agents.

First Responders Shape a Prompt and Sharp NF-κB-Mediated Transcriptional Response to TNF-α

Nuclear factor (NF)-κB controls the transcriptional response to inflammatory signals by translocating into the nucleus, but we lack a single-cell characterization of the resulting transcription dynamics. Here we show that upon tumor necrosis factor (TNF)-α transcription of NF-κB target genes is heterogeneous in individual cells but results in an average nascent transcription profile that is prompt (i.e., occurs almost immediately) and sharp (i.e., increases and decreases rapidly) compared with NF-κB nuclear localization. Using an NF-κB-controlled MS2 reporter we show that the single-cell nascent transcription is more heterogeneous than NF-κB translocation dynamics, with a fraction of synchronized “first responders” that shape the average transcriptional profile and are more prone to respond to multiple TNF-α stimulations. A mathematical model combining NF-κB-mediated gene activation and a gene refractory state is able to reproduce these features. Our work shows how the expression of target genes induced by transcriptional activators can be heterogeneous across single cells and yet time resolved on average.

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Nascent transcription upon TNF-α is heterogeneous, with a subset of “first responders”

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The average nascent transcription is prompt and sharper than NF-κB response

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First responders do not depend on NF-κB dynamics and respond more to pulsed stimuli

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A model including NF-κB and a gene refractory state reproduces these observations

Titanium-carbide MXenes for work function and interface engineering in perovskite solar cells

To improve the efficiency of perovskite solar cells, careful device design and tailored interface engineering are needed to enhance optoelectronic properties and the charge extraction process at the selective electrodes. Here, we use two-dimensional transition metal carbides (MXene Ti₃C₂T_x) with various termination groups (T_x) to tune the work function (WF) of the perovskite absorber and the TiO₂ electron transport layer (ETL), and to engineer the perovskite/ETL interface. Ultraviolet photoemission spectroscopy measurements and density functional theory calculations show that the addition of Ti₃C₂T_x to halide perovskite and TiO₂ layers permits the tuning of the materials' WFs without affecting other electronic properties. Moreover, the dipole induced by the Ti₃C₂T_x at the perovskite/ETL interface can be used to change the band alignment between these layers. The combined action of WF tuning and interface engineering can lead to substantial performance improvements in MXene-modified perovskite solar cells, as shown by the 26% increase of power conversion efficiency and hysteresis reduction with respect to reference cells without MXene.

Titanium-carbide MXenes for work function and interface engineering in perovskite solar cells

To improve the efficiency of perovskite solar cells, careful device design and tailored interface engineering are needed to enhance optoelectronic properties and the charge extraction process at the selective electrodes. Here, we use two-dimensional transition metal carbides (MXene Ti₃C₂T_x) with various termination groups (T_x) to tune the work function (WF) of the perovskite absorber and the TiO₂ electron transport layer (ETL), and to engineer the perovskite/ETL interface. Ultraviolet photoemission spectroscopy measurements and density functional theory calculations show that the addition of Ti₃C₂T_x to halide perovskite and TiO₂ layers permits the tuning of the materials' WFs without affecting other electronic properties. Moreover, the dipole induced by the Ti₃C₂T_x at the perovskite/ETL interface can be used to change the band alignment between these layers. The combined action of WF tuning and interface engineering can lead to substantial performance improvements in MXene-modified perovskite solar cells, as shown by the 26% increase of power conversion efficiency and hysteresis reduction with respect to reference cells without MXene.

Exploiting Live Imaging to Track Nuclei During Myoblast Differentiation and Fusion

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.

Graphene-Induced Improvements of Perovskite Solar Cell Stability: Effects on Hot-Carriers

Hot-carriers, that is, charge carriers with an effective temperature higher than that of the lattice, may contribute to the high power conversion efficiency (PCE) shown by perovskite-based solar cells (PSCs), which are now competitive with silicon solar cells. Hot-carriers lose their excess energy in very short times, typically in a few picoseconds after excitation. For this reason, the carrier dynamics occurring on this time scale are extremely important in determining the participation of hot-carriers in the photovoltaic process. However, the stability of PSCs over time still remains an issue that calls for a solution. In this work, we demonstrate that the insertion of graphene flakes into the mesoscopic TiO₂ scaffold leads to stable values of carrier temperature. In PSCs aged over 1 week, we indeed observe that in the graphene-free perovskite cells the carrier temperature decreases by about 500 K from 1800 to 1300 K, while the graphene-containing cell shows a reduction of less than 200 K after the same aging time delay. The stability of the carrier temperature reflects the stability of the perovskite nanocrystals embedded in the mesoporous graphene-TiO₂ layer. Our results, based on femtosecond transient absorption measurements, show that the insertion of graphene can be beneficial for the design of stable PSCs with the aim of exploiting the hot-carrier contribution to the PCE of the PSCs.

LPS-Challenged Macrophages Release Microvesicles Coated With Histones

Histones are the protein component of nucleosomes, which are the basic packing unit of chromatin. However, histones are also found in the blood, both as components of nucleosomes leaked out from dead cells, or expelled from neutrophils in the active process of NET formation. Circulating histones contribute to inflammation, and to lethality in sepsis, a hyperinflammatory condition, by interacting with specific receptors, notably toll-like receptor 4 (TLR4). Here, we show that histones are also actively released by LPS-activated macrophages in association with extracellular vesicles. Vesicle-associated histones can be recovered from the plasma of mice with sepsis. Actively released histones are on the outer surface of vesicles and can interact with TLR4. Thus, activated macrophages release histones without dying, at the same time, making their DNA more accessible and communicating to other cells that infection is present.

NF-κB, the Importance of Being Dynamic: Role and Insights in Cancer

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.

Single-cell analyses reveal an attenuated NF-κB response in the Salmonella-infected fibroblast

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 to Salmonella enterica serovar Typhimurium. Fibroblasts were used due to the capacity of S. 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 as IL1B, NFKBIA, TNFAIP3, and TRAF1 in uninfected (ST-) fibroblasts. These observations proved that S. Typhimurium dampens the NF-κB response in the infected fibroblast. Higher expression of SOCS3, encoding a "suppressor of cytokine signaling," was also observed in the ST+ population. Intracellular S. 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 of SOCS3 and all NF-κB target genes analyzed whereas T2 displayed no role in the control of SOCS3 and IL1B expression. Collectively, these data demonstrate that S. 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 for S. Typhimurium to establish intracellular persistent infections.

NF-κB oscillations translate into functionally related patterns of gene expression

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.

Interplay between stochasticity and negative feedback leads to pulsed dynamics and distinct gene activity patterns

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.

Aspirin's Active Metabolite Salicylic Acid Targets High Mobility Group Box 1 to Modulate Inflammatory Responses

Salicylic acid (SA) and its derivatives have been used for millennia to reduce pain, fever and inflammation. In addition, prophylactic use of acetylsalicylic acid, commonly known as aspirin, reduces the risk of heart attack, stroke and certain cancers. Because aspirin is rapidly de-acetylated by esterases in human plasma, much of aspirin's bioactivity can be attributed to its primary metabolite, SA. Here we demonstrate that human high mobility group box 1 (HMGB1) is a novel SA-binding protein. SA-binding sites on HMGB1 were identified in the HMG-box domains by nuclear magnetic resonance (NMR) spectroscopic studies and confirmed by mutational analysis. Extracellular HMGB1 is a damage-associated molecular pattern molecule (DAMP), with multiple redox states. SA suppresses both the chemoattractant activity of fully reduced HMGB1 and the increased expression of proinflammatory cytokine genes and cyclooxygenase 2 (COX-2) induced by disulfide HMGB1. Natural and synthetic SA derivatives with greater potency for inhibition of HMGB1 were identified, providing proof-of-concept that new molecules with high efficacy against sterile inflammation are attainable. An HMGB1 protein mutated in one of the SA-binding sites identified by NMR chemical shift perturbation studies retained chemoattractant activity, but lost binding of and inhibition by SA and its derivatives, thereby firmly establishing that SA binding to HMGB1 directly suppresses its proinflammatory activities. Identification of HMGB1 as a pharmacological target of SA/aspirin provides new insights into the mechanisms of action of one of the world's longest and most used natural and synthetic drugs. It may also provide an explanation for the protective effects of low-dose aspirin usage.

A computer method for the kinetic analysis of enzyme activity

A computer method is described in which an estimate of Km and V parameters is obtained by fitting a Michaelis-Menten hyperbola to experimental data. The frequency distribution of calculated parameters is far from normality. A statistical evaluation of the differences between kinetic parameters must be obtained by the use of non-parametric statistics.

Nucleosome loss facilitates the chemotactic response of macrophages

BACKGROUND

High mobility group box 1 (HMGB1) is a small nuclear protein with two functions. In the nucleus, it helps to wrap DNA around nucleosomes. When secreted, it recruits inflammatory cells and induces cytokine production. Before HMGB1 is secreted from inflammatory cells, it relocates to the cytoplasm, which partially or totally depletes cell nuclei of HMGB1. We previously showed that cells lacking HMGB1 contain 20% fewer nucleosomes and 30% more RNA transcripts levels genome-wide.

OBJECTIVE

We hypothesized that the depletion of nuclear HMGB1 plays a role in inflammation that can enhance or complement the role of extracellular HMGB1.

METHODS

We analysed the transcriptional profile of wild-type and Hmgb1-/- mouse embryonic fibroblasts (MEFs) as a proxy for cells that have lost HMGB1 from their nuclei. We explored the transcriptome of wild-type and Hmgb1-/- macrophages differentiated in the presence of granulocyte-macrophage colony-stimulating factor, before and after exposure to LPS/IFN-γ. In the same cells, histones and nuclear HMGB1 were quantified.

RESULTS

We found that Hmgb1-/- MEFs show a transcriptional profile associated with stress and inflammation responses. Moreover, wild-type macrophages that have secreted HMGB1 because of LPS/IFN-γ exposure rapidly reduce their histone content as much as cells that genetically lack HMGB1. Importantly, unstimulated Hmgb1-/- macrophages activate transcriptional pathways associated with cell migration and chemotaxis.

CONCLUSIONS

We suggest that nucleosome loss is an early event that facilitates transcriptional responses of macrophages to inflammation, particularly chemotaxis. HMGB1's dual roles in the nucleus and in the extracellular space appear to be complementary.

Histone content increases in differentiating embryonic stem cells

Mouse Embryonic Stem Cells (ESCs) are pluripotent mammalian cells derived from the Inner Cell Mass (ICM) of mouse blastocysts, which give rise to all three embryonic germ layers both in vivo and in vitro. Mouse ESCs have a distinct epigenetic landscape and a more decondensed chromatin compared to differentiated cells. Numerous studies have shown that distinct histone modifications in ESCs serve as hallmarks of pluripotency. However, so far it is still unknown whether the total histone content (as opposed to histone modifications) remains the same in cells of different developmental stage and differentiation capacity. In this work we show that total histone content differs between pluripotent and differentiated cells. In vitro spontaneous differentiation from ESCs to Embryoid Bodies (EBs) and directed differentiation toward neuronal and endodermal cells entails an increase in histone content. Primary MEFs also contain more histones than ESCs. We suggest that the difference in histone content is an additional hallmark of pluripotency, in addition to and besides histone modifications.

High-throughput analysis of NF-κB dynamics in single cells reveals basal nuclear localization of NF-κB and spontaneous activation of oscillations

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.

Receptor for Advanced Glycation Endproducts is upregulated in temporal lobe epilepsy and contributes to experimental seizures

Toll-like receptor 4 (TLR4) activation in neuron and astrocytes by High Mobility Group Box 1 (HMGB1) protein is a key mechanism of seizure generation. HMGB1 also activates the Receptor for Advanced Glycation Endproducts (RAGE), but it was unknown whether RAGE activation contributes to seizures or to HMGB1 proictogenic effects. We found that acute EEG seizures induced by 7ng intrahippocampal kainic acid (KA) were significantly reduced in Rage-/- mice relative to wild type (Wt) mice. The proictogenic effect of HMGB1 was decreased in Rage-/- mice, but less so, than in Tlr4-/- mice. In a mouse mesial temporal lobe epilepsy (mTLE) model, status epilepticus induced by 200ng intrahippocampal KA and the onset of the spontaneous epileptic activity were similar in Rage-/-, Tlr4-/- and Wt mice. However, the number of hippocampal paroxysmal episodes and their duration were both decreased in epileptic Rage-/- and Tlr4-/- mice vs Wt mice. All strains of epileptic mice displayed similar cognitive deficits in the novel object recognition test vs the corresponding control mice. CA1 neuronal cell loss was increased in epileptic Rage-/- vs epileptic Wt mice, while granule cell dispersion and doublecortin (DCX)-positive neurons were similarly affected. Notably, DCX neurons were preserved in epileptic Tlr4-/- mice. We did not find compensatory changes in HMGB1-related inflammatory signaling nor in glutamate receptor subunits in Rage-/- and Tlr4-/- naïve mice, except for ~20% NR2B subunit reduction in Rage-/- mice. RAGE was induced in neurons, astrocytes and microvessels in human and experimental mTLE hippocampi. We conclude that RAGE contributes to hyperexcitability underlying acute and chronic seizures, as well as to the proictogenic effects of HMGB1. RAGE and TLR4 play different roles in the neuropathologic sequelae developing after status epilepticus. These findings reveal new molecular mechanisms underlying seizures, cell loss and neurogenesis which involve inflammatory pathways upregulated in human epilepsy.

Rapamycin-sensitive signals control TCR/CD28-driven Ifng, Il4 and Foxp3 transcription and promoter region methylation

The mammalian target of rapamycin (mTOR) controls T-cell differentiation in response to polarizing cytokines. We previously found that mTOR blockade by rapamycin (RAPA) delays the G1-S cell cycle transition and lymphocyte proliferation. Here, we report that both mTOR complex 1 and mTOR complex 2 are readily activated following TCR/CD28 engagement and are critical for early expression of Ifng, Il4 and Foxp3, and for effector T cell differentiation in the absence of polarizing cytokines. While inhibition of mTOR complex 1 and cell division were evident at low doses of RAPA, inhibition of mTOR complex 2, Ifng, Il4 and Foxp3 expression, and T-cell polarization required higher doses and more prolonged treatments. We found that while T-bet and GATA3 were readily induced following TCR/CD28 engagement, administration of RAPA delayed their expression, and interfered with the loss of DNA methylation within Ifng and Il4 promoter regions. In contrast, RAPA prevented activation-dependent DNA methylation of the Foxp3 promoter favoring Foxp3 expression. As a result, RAPA-cultured cells lacked immediate effector functions and instead were enriched for IL-2+ cells. We propose that mTOR-signaling, by timing the expression of critical transcription factors and DNA methylation of proximal promoter regions, regulates transcriptional competence at immunologically relevant sites and hence lymphocyte differentiation.

Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output

The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. Nucleosome number in cells was considered fixed, but recently aging yeast and mammalian cells were shown to contain fewer nucleosomes. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker, and variant histones, and a correspondingly reduced number of nucleosomes, possibly because HMGB1 facilitates nucleosome assembly. Yeast nhp6 mutants lacking Nhp6a and -b proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and affects the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform and can be modelled assuming that different nucleosomal sites compete for available histones. Sites with a high propensity to occupation are almost always packaged into nucleosomes both in wild type and nucleosome-depleted cells; nucleosomes on sites with low propensity to occupation are disproportionately lost in nucleosome-depleted cells. We suggest that variation in nucleosome number, by affecting nucleosomal occupancy both genomewide and gene-specifically, constitutes a novel layer of epigenetic regulation.

The combination of marker gene swapping and fluorescence-activated cell sorting improves the efficiency of recombinant modified vaccinia virus Ankara vaccine production for human use

Modified vaccinia virus Ankara (MVA) is employed as a human vaccine vector for the high expression of heterologous genes and the lack of replication in mammalian cells. This study demonstrates that cells infected by recombinant viruses can be obtained by fluorescence-activated cell sorting. Recombinant viruses are generated by a swapping event between a red fluorescent protein gene in the acceptor virus and a plasmid cassette coding for both a green fluorescent marker and a transgene. To prevent the carry-over of parental virus, due to superinfection of the cells harbouring recombinant viruses, the sorting is performed on cells infected at low m.o.i. in the presence of a reversible inhibitor of viral particle release. Terminal dilution cloning is then used to isolate both green and marker-free recombinant viruses, which can be identified by whole-plate fluoroimaging. The differential visualization of all the viral types involved allows a stepwise monitoring of all recombinations and leads to a straightforward and efficient flow cytometry-based cell sorting purification protocol. As an example of the efficacy of this sorting procedure, the construction of rMVA's coding for the rat nuclear protein HMGB1 and H5N1 influenza A virus hemagglutinin is reported. The entire recombinant MVA production process is carried out in serum-free media employing primary chicken embryo fibroblasts (CEF), which are certified for the preparation of human vaccines. This rMVA production method is faster, simpler and more reliable than any other available procedure for obtaining safe vaccine stocks for human use.

Sustained oscillations of NF-kappaB produce distinct genome scanning and gene expression profiles

NF-kappaB is a prototypic stress-responsive transcription factor that acts within a complex regulatory network. The signaling dynamics of endogenous NF-kappaB in single cells remain poorly understood. To examine real time dynamics in living cells, we monitored NF-kappaB activities at multiple timescales using GFP-p65 knock-in mouse embryonic fibroblasts. Oscillations in NF-kappaB were sustained in most cells, with several cycles of transient nuclear translocation after TNF-alpha stimulation. Mathematical modeling suggests that NF-kappaB oscillations are selected over other non-oscillatory dynamics by fine-tuning the relative strengths of feedback loops like IkappaBalpha. The ability of NF-kappaB to scan and interact with the genome in vivo remained remarkably constant from early to late cycles, as observed by fluorescence recovery after photobleaching (FRAP). Perturbation of long-term NF-kappaB oscillations interfered with its short-term interaction with chromatin and balanced transcriptional output, as predicted by the mathematical model. We propose that negative feedback loops do not simply terminate signaling, but rather promote oscillations of NF-kappaB in the nucleus, and these oscillations are functionally advantageous.

Glycyrrhizin binds to high-mobility group box 1 protein and inhibits its cytokine activities

High-mobility group box 1 protein (HMGB1) is a nuclear component, but extracellularly it serves as a signaling molecule involved in acute and chronic inflammation, for example in sepsis and arthritis. The identification of HMGB1 inhibitors is therefore of significant experimental and clinical interest. We show that glycyrrhizin, a natural anti-inflammatory and antiviral triterpene in clinical use, inhibits HMGB1 chemoattractant and mitogenic activities, and has a weak inhibitory effect on its intranuclear DNA-binding function. NMR and fluorescence studies indicate that glycyrrhizin binds directly to HMGB1 (K(d) approximately 150 microM), interacting with two shallow concave surfaces formed by the two arms of both HMG boxes. Our results explain in part the anti-inflammatory properties of glycyrrhizin, and might direct the design of new derivatives with improved HMGB1-binding properties.

A hyper-dynamic equilibrium between promoter-bound and nucleoplasmic dimers controls NF-kappaB-dependent gene activity

Because of its very high affinity for DNA, NF-kappaB is believed to make long-lasting contacts with cognate sites and to be essential for the nucleation of very stable enhanceosomes. However, the kinetic properties of NF-kappaB interaction with cognate sites in vivo are unknown. Here, we show that in living cells NF-kappaB is immobilized onto high-affinity binding sites only transiently, and that complete NF-kappaB turnover on active chromatin occurs in less than 30 s. Therefore, promoter-bound NF-kappaB is in dynamic equilibrium with nucleoplasmic dimers; promoter occupancy and transcriptional activity oscillate synchronously with nucleoplasmic NF-kappaB and independently of promoter occupancy by other sequence-specific transcription factors. These data indicate that changes in the nuclear concentration of NF-kappaB directly impact on promoter function and that promoters sample nucleoplasmic levels of NF-kappaB over a timescale of seconds, thus rapidly re-tuning their activity. We propose a revision of the enhanceosome concept in this dynamic framework.

Tunneling as a stochastic process: a path-integral model for microwave experiments

Delay time results obtained in microwave experiments at frequencies above and below the cutoff frequency of different waveguide sections are interpreted on the basis of wave propagation in the presence of dissipative effects. Kac's original suggestion was the starting point for the formulation of a stochastic model, which has now been substantially improved, also in relation to the transition-elements theory of Feynman-Hibbs. In this way, an approach to the problem is provided, which is completely distinct from the ones formulated elsewhere.

HMG proteins: dynamic players in gene regulation and differentiation

Core histones package the genome into nucleosomes and control its accessibility to transcription factors. High mobility group proteins (HMGs) are, after histones, the second most abundant chromatin proteins and exert global genomic functions in establishing active or inactive chromatin domains. It is becoming increasingly clear that they also specifically control the expression of a limited number of genes. Moreover, they contribute to the fine tuning of transcription in response to rapid environmental changes. They do so by interacting with nucleosomes, transcription factors, nucleosome-remodelling machines, and with histone H1.

GR and HMGB1 interact only within chromatin and influence each other's residence time

Most nuclear proteins reside on a specific chromatin site only for seconds or less. The hit-and-run model of transcriptional control maintains that transcription complexes are assembled in a stochastic fashion from freely diffusible proteins; this contrasts to models involving stepwise assembly of stable holo complexes. However, the chances of forming a productive complex improve if the binding of one factor promotes the binding of its interactors. We prove here that in living cells, the glucocorticoid receptor and HMGB1 interact only within chromatin and not in the nucleoplasm and decrease each other's mobility. Thus, the formation of a GR-HMGB1-chromatin complex is more likely than one would expect from independent binding to chromatin of GR and HMGB1. Remarkably, this complex is potentially stable, and its disassembly is effected by active, ATP-consuming processes. We propose that kinetic cooperativity among transcription factors in chromatin binding may be a common feature in transcription and DNA transactions.

Monocytic cells hyperacetylate chromatin protein HMGB1 to redirect it towards secretion

High Mobility Group 1 protein (HMGB1) is a chromatin component that, when leaked out by necrotic cells, triggers inflammation. HMGB1 can also be secreted by activated monocytes and macrophages, and functions as a late mediator of inflammation. Secretion of a nuclear protein requires a tightly controlled relocation program. We show here that in all cells HMGB1 shuttles actively between the nucleus and cytoplasm. Monocytes and macrophages acetylate HMGB1 extensively upon activation with lipopolysaccharide; moreover, forced hyperacetylation of HMGB1 in resting macrophages causes its relocalization to the cytosol. Cytosolic HMGB1 is then concentrated by default into secretory lysosomes, and secreted when monocytic cells receive an appropriate second signal.

Association of chromatin proteins high mobility group box (HMGB) 1 and HMGB2 with mitotic chromosomes

High mobility group box (HMGB) 1 and 2 are two abundant nonhistone nuclear proteins that have been found in association with chromatin. Previous studies based on immunofluorescence analysis indicated that HMGB1 dissociates from chromosomes during mitosis. In the present work, HMGB1 and 2 subcellular localization was reinvestigated in living cells by using enhanced green fluorescent protein- and Discosome sp. red fluorescent protein-tagged proteins. Contrary to previous reports, HMGB1 and 2 were shown to be present under two forms in mitotic cells, i.e., free and associated with the condensed chromatin, which rapidly exchange. A detailed analysis of HMGB2 interaction with mitotic chromosomes indicated that two sites encompassing HMG-box A and B are responsible for binding. Importantly, this interaction was rapidly inactivated when cells were permeabilized or exposed to chemical fixatives that are widely used in immunodetection techniques. A comparable behavior was also observed for two proteins of the HMG-nucleosome binding (HMGN) group, namely, HMGN1 and HMGN2.

HMGB proteins and gene expression

High mobility group (HMG) proteins are chromatin proteins endowed with 'architectural' capabilities. HMGA proteins are moderately sequence-specific, and help build enhanceosomes by interacting with partner proteins and binding stably to the minor groove of DNA; their acetylation/deacetylation signal enhanceosome assembly or disassembly. HMGBs are much more dynamic proteins: they have no sequence specificity, and help transcription factors and other nuclear proteins bind to their cognate sites by bending the DNA molecule. However, HMGBs are rarely retained within the complex. Similarly, HMGBs interact with nucleosomes and promote their sliding, but remain bound only for fractions of a second. We argue that HMGBs fluidize chromatin - an action that appears opposite to that of histone H1.

HMGB1 interacts differentially with members of the Rel family of transcription factors

HMGB1 is an architectural factor that enhances the DNA binding affinity of several proteins. We have investigated the influence of HMGB1 on DNA binding by members of the Rel family. HMGB1 enhances DNA binding by p65/p50 and p50/p50, but reduces binding by p65/p65, c-Rel/c-Rel, p65/c-Rel, and p50/c-Rel. In pull-down assays, HMGB1 interacts directly with the p50 subunit via its HMG boxes and this interaction is weakened by the presence of the acidic tail. Functionally, HMGB1 is required for the NF-kappaB-dependent expression of the adhesion molecule VCAM-1.

Josephson junction coupled to a transmission line: a comparison of different approaches

The case of a Josephson junction loaded by a transmission line is reexamined, according to the Green's function method, in order to compare the results with those that we previously obtained, analytically and numerically, following a different procedure.

Dealing with discreteness: making 'exact' confidence intervals for proportions, differences of proportions, and odds ratios more exact

'Exact' methods for categorical data are exact in terms of using probability distributions that do not depend on unknown parameters. However, they are conservative inferentially. The actual error probabilities for tests and confidence intervals are bounded above by the nominal level. This article examines the conservatism for interval estimation and describes ways of reducing it. We illustrate for confidence intervals for several basic parameters, including the binomial parameter, the difference between two binomial parameters for independent samples, and the odds ratio and relative risk. Less conservative behavior results from devices such as (1) inverting tests using statistics that are 'less discrete', (2) inverting a single two-sided test rather than two separate one-sided tests each having size at least half the nominal level, (3) using unconditional rather than conditional methods (where appropriate) and (4) inverting tests using alternative p-values. The article concludes with recommendations for selecting an interval in three situations-when one needs to guarantee a lower bound on a coverage probability, when it is sufficient to have actual coverage probability near the nominal level, and when teaching in a classroom or consulting environment.

Anomalous delay in wave propagation and tunneling: a transition-elements analysis of the traversal time

An alternative model for near-field propagation and optical tunneling is proposed following the lines of the path-integral method developed by Feynman, and in particular by using a transition-elements analysis. Such a model was able to account for the frequency dependency of delay-time results of an experiment involving microwave propagation in the near field using two horn antennas [A. Ranfagni et al., Phys. Rev. E 66, 036111 (2002)]. Furthermore, this approach is also capable of interpreting delay-time results as a function of the barrier width in a frustrated total internal reflection experiment performed at the microwave scale and in the optical region.

Anomalous pulse delay in microwave propagation: A stochastic process interpretation

An experiment involving microwave propagation in the near-field region with two horn antennas demonstrated a superluminal behavior which is strongly dependent on the frequency. The models previously proposed are found to be inadequate for interpreting the results. An attempt is made within the framework of a stochastic model, which can be improved by a path-integral analysis.

Different approach for evaluating dissipation in macroscopic quantum tunneling

The problem of evaluating dissipative effects in macroscopic quantum tunneling is re-examined for the case of Josephson junctions, with the adoption of an alternative way with respect to several previously proposed and, in some cases, contradictory approaches. The system, which consists of a junction coupled to a transmission line, is analyzed both analytically and numerically. A test of the theoretical model, as compared to the experimental results available, is performed in accordance with a criterion based on a shortening of the traversal time.

Simple stochastic model for optical tunneling

A simple model, derived from a Brownian-motion scheme, is capable of interpreting the results of delay-time measurements relative to frustrated total reflection experiments at the microwave scale but also in the visible region. In this framework we also obtain a plausible description of the trajectories (rays) inside the tunneling region, the air gap between two paraffin prisms.

c-Rel is a selective activator of a novel IL-4/CD40 responsive element in the human Ig gamma4 germline promoter

Induction of isotype switching to a specific C(H) gene correlates with the transcriptional activation of the same gene in germline (GL) configuration. Expression of correctly spliced GL transcripts is necessary to target a switch region for recombination. In human B cells, the IgE and IgG4 isotypes are both induced by IL-4 through sequential switching, but are functionally antagonistic because IgG4 appears to have IgE-blocking activity. In order to understand the molecular mechanisms that regulate IgG4 production, we undertook a systematic analysis of the gamma4 GL promoter. A HindIII/NaeI region (-421/+474) highly conserved in the human gamma locus mediated the synergistic activation of a reporter gene in response to IL-4 and CD40 cross-linking. STAT6 binding to the proximal gamma4 GL promoter was essential for both IL-4-induced activation and CD40-dependent enhancement of transcription. Of note, a 45bp region (-76/-32) centered around the STAT6 binding motif drove robust synergistic activation of a heterologous fos promoter upon stimulation with IL-4 and CD40 cross-linking. This finding suggested that the (-76/-32) region may contain a novel IL-4/CD40 responsive element (RE). Electrophoretic mobility shift assays (EMSA) analysis using BL-2 nuclear extracts and in vitro translated NF-kappaB/Rel family proteins revealed the presence of a motif that overlaps the 5' end of the STAT6 element and binds selectively c-Rel. A mutation that abrogated c-Rel, but not STAT6, binding strongly impaired the CD40-induced enhancement of IL-4-dependent gamma4 GL transcription in reporter assays. These results indicate that c-Rel is selectively involved in the CD40-dependent activation of the IL-4/CD40 RE in the proximal gamma4 GL promoter.

Exact inference for categorical data: recent advances and continuing controversies

Methods for exact small-sample analyses with categorical data have been increasingly well developed in recent years. A variety of exact methods exist, primarily using the approach that eliminates unknown parameters by conditioning on their sufficient statistics. In addition, a variety of algorithms now exist for implementing the methods. This paper briefly summarizes the exact approaches and describes recent developments. Controversy continues about the appropriateness of some exact methods, primarily relating to their conservative nature because of discreteness. This issue is examined for two simple problems in which discreteness can be severe--interval estimation of a proportion and the odds ratio. In general, adjusted exact methods based on the mid-P-value seem a reasonable way of reducing the severity of this problem.

On small-sample confidence intervals for parameters in discrete distributions

The traditional definition of a confidence interval requires the coverage probability at any value of the parameter to be at least the nominal confidence level. In constructing such intervals for parameters in discrete distributions, less conservative behavior results from inverting a single two-sided test than inverting two separate one-sided tests of half the nominal level each. We illustrate for a variety of discrete problems, including interval estimation of a binomial parameter, the difference and the ratio of two binomial parameters for independent samples, and the odds ratio.

Experimental evidence of tunneling as a stochastic process

A model for tunneling based on stochastic processes proves to be capable of interpreting the results of two experiments at the microwave scale. The first of these consisted of measuring the penetration time in a subcutoff waveguide; the second one, in measuring the shift of a beam in a frustrated total reflection. Said shift which is a measurement of the traversal time of the barrier. In both cases, a peak in the real-time component was evidenced, as predicted by the theoretical model.