Fernand Hayot

Chromosome-specific and noisy IFNB1 transcription in individual virus-infected human primary dendritic cells

The induction of interferon beta (IFNB1) is a key event in the antiviral immune response. We studied the role of transcriptional noise in the regulation of the IFNB1 locus in primary cultures of human dendritic cells (DCs), which are important ‘first responders’ to viral infection. In single cell assays, IFNB1 mRNA expression in virus-infected DCs showed much greater cell-to-cell variation than that of a housekeeping gene, another induced transcript and viral RNA. We determined the contribution of intrinsic noise by measuring the allelic origin of transcripts in each cell and found that intrinsic noise is a very significant part of total noise. We developed a stochastic model to investigate the underlying mechanisms. We propose that the surprisingly high levels of IFNB1 transcript noise originate from the complexity of IFNB1 enhanceosome formation, which leads to a range up to many minutes in the differences within each cell in the time of activation of each allele.

A simple model of retina-LGN transmission

To gain a deeper understanding of the transmission of visual signals from retina through the lateral geniculate nucleus (LGN), we have used a simple leaky integrate and-fire model to simulate a relay cell in the LGN. The simplicity of the model was motivated by two questions: (1) Can an LGN model that is driven by a retinal spike train recorded as synaptic (‘S’) potentials, but does not include a diverse array of ion channels, nor feedback inputs from the cortex, brainstem, and thalamic reticular nucleus, accurately simulate the LGN discharge on a spike-for-spike basis? (2) Are any special synaptic mechanisms, beyond simple summation of currents, necessary to model experimental recordings? We recorded cat relay cell responses to spatially homogeneous small or large spots, with luminance that was rapidly modulated in a pseudo-random fashion. Model parameters for each cell were optimized with a Simplex algorithm using a short segment of the recording. The model was then tested on a much longer, distinct data set consisting of responses to numerous repetitions of the noisy stimulus. For LGN cells that spiked in response to a sufficiently large fraction of retinal inputs, we found that this simplified model accurately predicted the firing times of LGN discharges. This suggests that modulations of the efficacy of the retino-geniculate synapse by pre-synaptic facilitation or depression are not necessary in order to account for the LGN responses generated by our stimuli, and that post-synaptic summation is sufficient.

Mixed Analog/Digital Gonadotrope Biosynthetic Response to Gonadotropin-releasing Hormone

Mammalian reproduction requires gonadotropin-releasing hormone (GnRH)-mediated signaling from brain neurons to pituitary gonadotropes. Because the pulses of released GnRH vary greatly in amplitude, we studied the biosynthetic response of the gonadotrope to varying GnRH concentrations, focusing on extracellular-regulated kinase (ERK) phosphorylation and egr1 mRNA and protein production. The overall average level of ERK activation in populations of cells increased non-cooperatively with increasing GnRH and did not show evidence of either ultrasensitivity or bistability. However, automated image analysis of single-cell responses showed that whereas individual gonadotropes exhibited two response states, inactive and active, both the probability of activation and the average response in activated cells increased with increasing GnRH concentration. These data indicate a hybrid single-cell response having both digital (switch-like) and analog (graded) features. Mathematical modeling suggests that the hybrid response can be explained by indirect thresholding of ERK activation resulting from the distributed structure of the GnRH-modulated network. The hybrid response mechanism improves the reliability of noisy reproductive signal transmission from the brain to the pituitary.

Role of Cell-to-Cell Variability in Activating a Positive Feedback Antiviral Response in Human Dendritic Cells

In the first few hours following Newcastle disease viral infection of human monocyte-derived dendritic cells, the induction of IFNB1 is extremely low and the secreted type I interferon response is below the limits of ELISA assay. However, many interferon-induced genes are activated at this time, for example DDX58 (RIGI), which in response to viral RNA induces IFNB1. We investigated whether the early induction of IFNBI in only a small percentage of infected cells leads to low level IFN secretion that then induces IFN-responsive genes in all cells. We developed an agent-based mathematical model to explore the IFNBI and DDX58 temporal dynamics. Simulations showed that a small number of early responder cells provide a mechanism for efficient and controlled activation of the DDX58-IFNBI positive feedback loop. The model predicted distributions of single cell responses that were confirmed by single cell mRNA measurements. The results suggest that large cell-to-cell variation plays an important role in the early innate immune response, and that the variability is essential for the efficient activation of the IFNB1 based feedback loop.

Proapoptotic and Antiapoptotic Actions of Stat1 versus Stat3 Underlie Neuroprotective and Immunoregulatory Functions of IL-11

Current therapies for multiple sclerosis target inflammation but do not directly address oligodendrocyte protection or myelin repair. The gp130 family cytokines ciliary neurotrophic factor, leukemia inhibitory factor, and IL-11 have been identified as oligodendrocyte growth factors, and IL-11 is also strongly immunoregulatory, but their underlying mechanisms of action are incompletely characterized. In this study, we demonstrate that these effects of IL-11 are mediated via differential regulation of apoptosis in oligodendrocytes versus Ag-presenting dendritic cells (DCs), and are dependent on lineage-specific activity of the transcription factors Stat1 versus Stat3. Focal demyelinating lesions induced in cerebral cortices of IL-11Rα−/− mice using stereotactic microinjection of lysolecithin were larger than in controls, and remyelination was delayed. In IL-11Rα−/− mice, lesions displayed extensive oligodendrocyte loss and axonal transection, and increased infiltration by inflammatory cells including CD11c+ DCs, CD3+ lymphocytes, and CD11b+ phagocytes. In oligodendrocyte progenitor cell (OPC) cultures, IL-11 restricted caspase 9 activation and apoptosis, and it increased myelination in OPC-neuron cocultures. Importantly, siRNA inhibition of Stat1 enhanced the antiapoptotic effects of IL-11 on OPCs, but IL-11 induced apoptosis in the presence of Stat3 silencing. In contrast, IL-11 augmented caspase activation and apoptosis in cultures of CD11c+ DCs, but not in CD11b+ or CD3+ cells. Inhibition of Stat3 exacerbated the proapoptotic effects of IL-11 on DCs, whereas they were ablated in Stat1−/− cultures. Collectively, these findings reveal novel mechanisms underlying the actions of a neuroprotective and immunoregulatory member of the gp130 cytokine family, suggesting avenues to enhance oligodendrocyte viability and restrict CNS inflammation in multiple sclerosis.

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-β response to viral infection

Signals produced by early responding cells to viral infection calibrate the immune response of the cell population. Taking the time to respond One of the earliest responses of cells to viral infection is expression of the gene encoding interferon-β (Ifnb1). Within a population of cells exposed to virus, the overall immune response is shaped by the percentage of cells that become infected, the proportion of those infected cells that initially express Ifnb1, and the extent of Ifnb1 expression per cell. Patil et al. used single-cell imaging to quantify the amounts of Ifnb1 and viral mRNAs in infected human dendritic cells over time. Mathematical simulations of viral infection indicated that differences in the timing of Ifnb1 induction in individual cells contributed to the dynamics of the population. Indeed, further experiments showed that the earliest responders released paracrine signals that controlled the timing of the antiviral response of the remaining cells within the population. These results have implications for understanding how individual immune cells coordinate the extent of the immune response to viral infection. Immune responses to viral infection are stochastic processes, which initiate in a limited number of cells that then propagate the response. A key component of the response to viral infection entails the synthesis and secretion of type I interferons (IFNs), including the early induction of the gene encoding IFN-β (Ifnb1). With single-cell analysis and mathematical modeling, we investigated the mechanisms underlying how increases in the amount of Ifnb1 mRNA per cell and in the numbers of cells expressing Ifnb1 calibrate the response to viral infection. We used single-cell, single-molecule assays to quantify the early induction of Ifnb1 expression (the Ifnb1 response) in human monocyte-derived dendritic cells infected with Newcastle disease virus, thus retaining the physiological stoichiometry of transcriptional regulators to both alleles of the Ifnb1 gene. We applied computational methods to extract the stochastic features that underlie the cell-to-cell variations in gene expression over time. Integration of simulations and experiments identified the role of paracrine signaling in increasing the number of cells that express Ifnb1 over time and in calibrating the immune response to viral infection.

Combinatorial actions of Tgfβ and Activin ligands promote oligodendrocyte development and CNS myelination.

In the embryonic CNS, development of myelin-forming oligodendrocytes is limited by bone morphogenetic proteins, which constitute one arm of the transforming growth factor-β (Tgfβ) family and signal canonically via Smads 1/5/8. Tgfβ ligands and Activins comprise the other arm and signal via Smads 2/3, but their roles in oligodendrocyte development are incompletely characterized. Here, we report that Tgfβ ligands and activin B (ActB) act in concert in the mammalian spinal cord to promote oligodendrocyte generation and myelination. In mouse neural tube, newly specified oligodendrocyte progenitors (OLPs) are first exposed to Tgfβ ligands in isolation, then later in combination with ActB during maturation. In primary OLP cultures, Tgfβ1 and ActB differentially activate canonical Smad3 and non-canonical MAP kinase signaling. Both ligands enhance viability, and Tgfβ1 promotes proliferation while ActB supports maturation. Importantly, co-treatment strongly activates both signaling pathways, producing an additive effect on viability and enhancing both proliferation and differentiation such that mature oligodendrocyte numbers are substantially increased. Co-treatment promotes myelination in OLP-neuron co-cultures, and maturing oligodendrocytes in spinal cord white matter display strong Smad3 and MAP kinase activation. In spinal cords of ActB-deficient Inhbb−/− embryos, apoptosis in the oligodendrocyte lineage is increased and OLP numbers transiently reduced, but numbers, maturation and myelination recover during the first postnatal week. Smad3−/− mice display a more severe phenotype, including diminished viability and proliferation, persistently reduced mature and immature cell numbers, and delayed myelination. Collectively, these findings suggest that, in mammalian spinal cord, Tgfβ ligands and ActB together support oligodendrocyte development and myelin formation.

Immune Response Modeling of Interferon β-Pretreated Influenza Virus-Infected Human Dendritic Cells

The pretreatment of human dendritic cells with interferon-beta enhances their immune response to influenza virus infection. We measured the expression levels of several key players in that response over a period of 13 h both during pretreatment and after viral infection. Their activation profiles reflect the presence of both negative and positive feedback loops in interferon induction and interferon signaling pathway. Based on these measurements, we have developed a comprehensive computational model of cellular immune response that elucidates its mechanism and its dynamics in interferon-pretreated dendritic cells, and provides insights into the effects of duration and strength of pretreatment.

Stimulus size dependence of information transfer from retina to thalamus

Relay cells in the mammalian lateral geniculate nucleus (LGN) are driven primarily by single retinal ganglion cells (RGCs). However, an LGN cell responds typically to less than half of the spikes it receives from the RGC that drives it, and without retinal drive the LGN is silent (Kaplan and Shapley, 1984). Recent studies, which used stimuli restricted to the receptive field (RF) center, show that despite the great loss of spikes, more than half of the information carried by the RGC discharge is typically preserved in the LGN discharge (Sincich et al., 2009), suggesting that the retinal spikes that are deleted by the LGN carry less information than those that are transmitted to the cortex. To determine how LGN relay neurons decide which retinal spikes to respond to, we recorded extracellularly from the cat LGN relay cell spikes together with the slow synaptic (‘S’) potentials that signal the firing of retinal spikes. We investigated the influence of the inhibitory surround of the LGN RF by stimulating the eyes with spots of various sizes, the largest of which covered the center and surround of the LGN relay cells RF. We found that for stimuli that activated mostly the RF center, each LGN spike delivered more information than the retinal spike, but this difference was reduced as stimulus size increased to cover the RF surround. To evaluate the optimality of the LGN editing of retinal spikes, we created artificial spike trains from the retinal ones by various deletion schemes. We found that single LGN cells transmitted less information than an optimal detector could.

Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses.

ABSTRACT Influenza viruses continue to present global threats to human health. Antigenic drift and shift, genetic reassortment, and cross-species transmission generate new strains with differences in epidemiology and clinical severity. We compared the temporal transcriptional responses of human dendritic cells (DC) to infection with two pandemic (A/Brevig Mission/1/1918, A/California/4/2009) and two seasonal (A/New Caledonia/20/1999, A/Texas/36/1991) H1N1 influenza viruses. Strain-specific response differences included stronger activation of NF-κB following infection with A/New Caledonia/20/1999 and a unique cluster of genes expressed following infection with A/Brevig Mission/1/1918. A common antiviral program showing strain-specific timing was identified in the early DC response and found to correspond with reported transcript changes in blood during symptomatic human influenza virus infection. Comparison of the global responses to the seasonal and pandemic strains showed that a dramatic divergence occurred after 4 h, with only the seasonal strains inducing widespread mRNA loss. IMPORTANCE Continuously evolving influenza viruses present a global threat to human health; however, these host responses display strain-dependent differences that are incompletely understood. Thus, we conducted a detailed comparative study assessing the immune responses of human DC to infection with two pandemic and two seasonal H1N1 influenza strains. We identified in the immune response to viral infection both common and strain-specific features. Among the stain-specific elements were a time shift of the interferon-stimulated gene response, selective induction of NF-κB signaling by one of the seasonal strains, and massive RNA degradation as early as 4 h postinfection by the seasonal, but not the pandemic, viruses. These findings illuminate new aspects of the distinct differences in the immune responses to pandemic and seasonal influenza viruses.