scholarly journals Mathematical modelling of activation-induced heterogeneity reveals cell state transitions underpinning macrophage responses to LPS

2021 ◽  
Author(s):  
Shoumit Dey ◽  
Dave Boucher ◽  
Jonathan William Pitchford ◽  
Dimitris Lagos

Despite extensive work on macrophage heterogeneity, the mechanisms driving activation induced heterogeneity (AIH) in macrophages remain poorly understood. Here, we use two in vitro cellular models of LPS-induced tolerance (bone marrow-derived macrophages or BMDMs and RAW 264.7 cells), single-cell protein measurements, and mathematical modelling to explore how AIH underpins primary and secondary responses to LPS. We measure expression of TNF, IL-6, pro-IL-1β, and NOS2 and demonstrate that macrophage community AIH is dependent on LPS dose. We show that altered AIH kinetics in macrophages responding to a second LPS challenge underpin hypo-responsiveness to LPS. These empirical data can be explained by a mathematical 3-state model including negative, positive, and non-responsive states (NRS), but they are also compatible with a 4-state model that includes distinct reversibly NRS and non-responsive permanently states (NRPS). Our mathematical model, termed NoRM (Non-Responsive Macrophage) model identifies similarities and differences between BMDM and RAW 264.7 cell responses. In both cell types, transition rates between states in the NoRM model are distinct for each of the tested proteins and, crucially, macrophage hypo-responsiveness is underpinned by changes in transition rates to and from NRS. Overall, our findings provide support for a critical role for phenotypically negative macrophage populations as an active component of AIH and primary and secondary responses to LPS. This reveals unappreciated aspects of cellular ecology and community dynamics associated with LPS-driven training of macrophages.

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Pei-Fang Lai ◽  
Ching-Feng Cheng ◽  
Heng Lin ◽  
Tzu-Ling Tseng ◽  
Hsi-Hsien Chen ◽  
...  

Lipopolysaccharide (LPS) triggers innate immunity mainly via TLR4 signaling. ATF3 is a negative regulator of TLR4 signaling. HMGB1 plays a critical role in the final step of sepsis. However, the mechanisms of ATF3 and the role of HMGB1 in regulating innate immunity-induced sepsis are incompletely understood. In this study, we found that serum HMGB1 levels were 10-fold higher in patients with sepsis than normal controls. We further demonstrated that ATF3 gene knockout in mice subjected to LPS-induced endotoxemia correlates with an increase in the mortality rate and the elevated expression of IL-6, TNF-α, NO, MCP-1, and HMGB1 in the lung tissues or serum. The biochemical effects of ATF3 were observed inin vitromacrophages and blocked by ATF3 siRNA treatment. We have also shown that adeno-associated virus-mediated ATF3 gene transfer protected ATF3 knockout mice from LPS-induced mortality. In addition, ATF3 knockdown increased LPS-induced release of HMGB1. In conclusion, upregulation of ATF3 contributes to the reduced release of inflammatory molecules, especially HMGB1, which induced lung injury and increased the survival rate of mice after LPS challenge. Therefore, suppressing LPS-induced inflammation with ATF3 induction or ATF3 mimetics may be an important strategy for sepsis therapy.


BMC Medicine ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Shu-zhen Zhang ◽  
Qin-qin Wang ◽  
Qiao-qiao Yang ◽  
Huan-yu Gu ◽  
Yan-qing Yin ◽  
...  

Abstract Background Brain innate immunity is vital for maintaining normal brain functions. Immune homeostatic imbalances play pivotal roles in the pathogenesis of neurological diseases including Parkinson’s disease (PD). However, the molecular and cellular mechanisms underlying the regulation of brain innate immunity and their significance in PD pathogenesis are still largely unknown. Methods Cre-inducible diphtheria toxin receptor (iDTR) and diphtheria toxin-mediated cell ablation was performed to investigate the impact of neuron-glial antigen 2 (NG2) glia on the brain innate immunity. RNA sequencing analysis was carried out to identify differentially expressed genes in mouse brain with ablated NG2 glia and lipopolysaccharide (LPS) challenge. Neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mice were used to evaluate neuroinflammatory response in the presence or absence of NG2 glia. The survival of dopaminergic neurons or glial cell activation was evaluated by immunohistochemistry. Co-cultures of NG2 glia and microglia were used to examine the influence of NG2 glia to microglial activation. Results We show that NG2 glia are required for the maintenance of immune homeostasis in the brain via transforming growth factor-β2 (TGF-β2)-TGF-β type II receptor (TGFBR2)-CX3C chemokine receptor 1 (CX3CR1) signaling, which suppresses the activation of microglia. We demonstrate that mice with ablated NG2 glia display a profound downregulation of the expression of microglia-specific signature genes and remarkable inflammatory response in the brain following exposure to endotoxin lipopolysaccharides. Gain- or loss-of-function studies show that NG2 glia-derived TGF-β2 and its receptor TGFBR2 in microglia are key regulators of the CX3CR1-modulated immune response. Furthermore, deficiency of NG2 glia contributes to neuroinflammation and nigral dopaminergic neuron loss in MPTP-induced mouse PD model. Conclusions These findings suggest that NG2 glia play a critical role in modulation of neuroinflammation and provide a compelling rationale for the development of new therapeutics for neurological disorders.


Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2124 ◽  
Author(s):  
Erna Sulistyowati ◽  
Mei-Yueh Lee ◽  
Lin-Chi Wu ◽  
Jong-Hau Hsu ◽  
Zen-Kong Dai ◽  
...  

Heat shock cognate protein 70 (HSC70), a molecular chaperone, is constitutively expressed by mammalian cells to regulate various cellular functions. It is associated with many diseases and is a potential therapeutic target. Although HSC70 also possesses an anti-inflammatory action, the mechanism of this action remains unclear. This current study aimed to assess the anti-inflammatory effects of HSC70 in murine macrophages RAW 264.7 exposed to lipopolysaccharides (LPS) and to explain its pathways. Mouse macrophages (RAW 264.7) in 0.1 µg/mL LPS incubation were pretreated with recombinant HSC70 (rHSC70) and different assays (Griess assay, enzyme-linked immune assay/ELISA, electrophoretic mobility shift assay/EMSA, gelatin zymography, and Western blotting) were performed to determine whether rHSC70 blocks pro-inflammatory mediators. The findings showed that rHSC70 attenuated the nitric oxide (NO) generation, tumor necrosis factor α (TNF-α) and interleukin 6 (IL-6) expressions in LPS-stimulated RAW264.7 cells. In addition, rHSC70 preconditioning suppressed the activities and expressions of matrix metalloproteinase-2 (MMP-2) and MMP-9. Finally, rHSC70 diminished the nuclear translocation of nuclear factor-κB (NF-κB) and reduced the phosphorylation of extracellular-signal regulated kinases 1/2 (ERK1/2), c-Jun N-terminal kinase (JNK), p38 mitogen-activated protein kinases (MAPK), and phosphatidylinositol-3-kinase (PI3K/Akt). We demonstrate that rHSC70 preconditioning exerts its anti-inflammatory effects through NO production constriction; TNF-α, and IL-6 suppression following down-regulation of inducible nitric oxide synthase (iNOS), cyclooxygenase 2 (COX-2), and MMP-2/MMP-9. Accordingly, it ameliorated the signal transduction of MAPKs, Akt/IκBα, and NF-κB pathways. Therefore, extracellular HSC70 plays a critical role in the innate immunity modulation and mechanisms of endogenous protective stimulation.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3929-3929
Author(s):  
R. P. Weitzel ◽  
Y. Huang ◽  
L. Fanning ◽  
M. Kozik ◽  
P. Leahy ◽  
...  

Abstract Background. Graft versus host disease (GVHD) after allogeneic stem cell transplantation is associated with significant morbidity and mortality and targeted therapies are needed. The transcription factor nuclear factor of activated T-cells 1 (NFAT1) is known to interact with various other proteins, including AP-1 (fos/jun heterodimer), regulating both active immune responses and T-cell anergy. We have previously demonstrated lower expression of NFAT-associated transcripts via microarray, including IFN-γ, TNF-α, M-CSF, IL-3, 4, 5, and 13, IL-2R-α, CD40L, MIP1-α, as well as related transcription factors such as JunB, FOSL1, STAT4, T-bet, and c-maf in umbilical cord blood (UCB) CD4+ cells following primary stimulation when compared to cells obtained from adult blood (AB). We hypothesize a critical role for these NFAT1-dependent factors in the increased proliferation, decreased cytokine production seen in UCB, and lower incidence of GVHD following UCB transplantation. Here we present data more closely exploring the behavior of NFAT1 and associated genes in both UCB and AB CD4+ T-cells following primary stimulation. Methods. siRNA targeting NFAT1 mRNA was utilized to study the effects of lowered NFAT1 in primary human T-cells. CD14neg/4+ T-cells were isolated from adult peripheral blood by ficoll density gradient and selection by MACS. These cells were then immediately transfected via Nucleofector electroporation (Amaxa Biosystems, Gaithersburg, MD) with siRNA duplexes targeting NFAT1 and Cyclophilin B as well as an eGFP-encoding plasmid along with appropriate controls. Cultures were stimulated by anti-CD3/CD28 for 16h. 24h following transfection. Whole cell protein was harvested from a portion of each culture, and the remaining cells washed with PBS and replaced in non-stimulating media. Protein was extracted from the remaining cells 24h later. Protein lysate was analyzed by western blot for NFAT1, Cyclophilin-B, and β-Actin. Separately, expression of 7 transcripts (FOS, JUN, JUNB, FOSL1, BACH2, NFAM, and NFAT1) was analyzed via real-time PCR (RT-PCR). mRNA was obtained from 4 UCB and 4 AB samples at baseline (0h) (n=2) and 16h (n=2) of stimulation, using β-2-microglobulin as an endogenous control. Results. Transfection efficiency was measured to be approximately 70% via fluorescence microscopy of the eGFP-transfected culture. Our data indicate marginal reduction of NFAT1 protein at 24h. Notably after 48h approximately 65% knockdown is evident. Time course studies to determine the stability of siRNA-mediated NFAT1 knockdown are ongoing. No significant increase in the level of NFAT1 mRNA as measured by RT-PCR was detected. This suggests that the increase in NFAT1 protein levels post stimulation may not be a result of transcriptional regulation. Both UCB and AB samples exhibited a strong (15 fold) increase in FOSL1 transcription, and confirmed the enhanced up-regulation (about 3 fold) in the AB sample seen in microarray. Conclusions. Our data elucidate differences in the transcriptional program between UCB and AB T-cells, suggesting a crucial role for post-transcriptional events in the regulation of NFAT1 and its associated genes. Our findings identify differing regulation and expression of transcription factors in UCB vs. AB T-cells that may underlie the lower incidence and severity of GVHD seen in patients infused with UCB-derived grafts, and implicate additional elements which may modulate UCB T-cell alloreactivity. Studies to analyze the direct effects of decreased NFAT1 expression on relevant cytokines and other signaling molecules are currently ongoing.


2010 ◽  
Vol 139 (6) ◽  
pp. 836-848 ◽  
Author(s):  
H. RAHMANDAD ◽  
K. HU ◽  
R. J. DUINTJER TEBBENS ◽  
K. M. THOMPSON

SUMMARYWe developed an individual-based (IB) model to explore the stochastic attributes of state transitions, the heterogeneity of the individual interactions, and the impact of different network structure choices on the poliovirus transmission process in the context of understanding the dynamics of outbreaks. We used a previously published differential equation-based model to develop the IB model and inputs. To explore the impact of different types of networks, we implemented a total of 26 variations of six different network structures in the IB model. We found that the choice of network structure plays a critical role in the model estimates of cases and the dynamics of outbreaks. This study provides insights about the potential use of an IB model to support policy analyses related to managing the risks of polioviruses and shows the importance of assumptions about network structure.


2018 ◽  
Author(s):  
Stephanie E. Jones ◽  
Christine A. Pham ◽  
Joseph McKillip ◽  
Matthew Zambri ◽  
Erin E. Carlson ◽  
...  

ABSTRACTBacteria and fungi produce a wide array of volatile organic compounds (VOCs), and these can act as infochemicals or as competitive tools. Recent work has shown that the VOC trimethylamine (TMA) can promote a new form ofStreptomycesgrowth, termed ‘exploration’. Here, we report that TMA also serves to alter nutrient availability in the area surrounding exploring cultures: TMA dramatically increases the environmental pH, and in doing so, reduces iron availability. This, in turn, compromised the growth of other soil bacteria and fungi. In contrast,Streptomycesthrives in these iron-depleted niches by secreting a suite of differentially modified siderophores, and by upregulating genes associated with siderophore uptake. Further reducing iron levels by siderophore piracy, limiting siderophore uptake, or growing cultures in the presence of iron chelators, unexpectedly enhanced exploration. Our work reveals a new role for VOCs in modulating iron levels in the environment, and implies a critical role for VOCs in modulating the behaviour of microbes and the makeup of their communities.


2021 ◽  
Vol 17 (11) ◽  
pp. e1009606
Author(s):  
Diego Barra Avila ◽  
Juan R. Melendez-Alvarez ◽  
Xiao-Jun Tian

The Hippo-YAP/TAZ signaling pathway plays a critical role in tissue homeostasis, tumorigenesis, and degeneration disorders. The regulation of YAP/TAZ levels is controlled by a complex regulatory network, where several feedback loops have been identified. However, it remains elusive how these feedback loops contain the YAP/TAZ levels and maintain the system in a healthy physiological state or trap the system in pathological conditions. Here, a mathematical model was developed to represent the YAP/TAZ regulatory network. Through theoretical analyses, three distinct states that designate the one physiological and two pathological outcomes were found. The transition from the physiological state to the two pathological states is mechanistically controlled by coupled bidirectional bistable switches, which are robust to parametric variation and stochastic fluctuations at the molecular level. This work provides a mechanistic understanding of the regulation and dysregulation of YAP/TAZ levels in tissue state transitions.


Author(s):  
Ivan A. Kuznetsov ◽  
Andrey V. Kuznetsov

This paper develops a simplified analytical solution for the slow axonal transport of tau proteins. A six kinetic state model developed in Jung and Brown [1] was used to simulate transport of tau. The model was extended by accounting for tau degradation and diffusion in the off-track kinetic states. The analytical solution was obtained by assuming that transitions between anterograde and retrograde states are infrequent. This assumption was validated through an analysis of the sensitivity of the solution to changes in the values of the two kinetic constants that describe the transition rates between the anterograde and retrograde states, and by a comparison with the experimentally measured tau distributions reported in Konzack et al. [2]. The predicted average transport velocity of tau was also in the experimentally reported range.


mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Stephanie E. Jones ◽  
Christine A. Pham ◽  
Matthew P. Zambri ◽  
Joseph McKillip ◽  
Erin E. Carlson ◽  
...  

ABSTRACTBacteria and fungi produce a wide array of volatile organic compounds (VOCs), and these can act as chemical cues or as competitive tools. Recent work has shown that the VOC trimethylamine (TMA) can promote a new form ofStreptomycesgrowth, termed “exploration.” Here, we report that TMA also serves to alter nutrient availability in the area surrounding exploring cultures: TMA dramatically increases the environmental pH and, in doing so, reduces iron availability. This, in turn, compromises the growth of other soil bacteria and fungi. In response to this low-iron environment,Streptomyces venezuelaesecretes a suite of differentially modified siderophores and upregulates genes associated with siderophore uptake. Further reducing iron levels by limiting siderophore uptake or growing cultures in the presence of iron chelators enhanced exploration. Exploration was also increased whenS. venezuelaewas grown in association with the related low-iron- and TMA-tolerantAmycolatopsisbacteria, due to competition for available iron. We are only beginning to appreciate the role of VOCs in natural communities. This work reveals a new role for VOCs in modulating iron levels in the environment and implies a critical role for VOCs in modulating the behavior of microbes and the makeup of their communities. It further adds a new dimension to our understanding of the interspecies interactions that influenceStreptomycesexploration and highlights the importance of iron in exploration modulation.IMPORTANCEMicrobial growth and community interactions are influenced by a multitude of factors. A new mode ofStreptomycesgrowth—exploration—is promoted by interactions with the yeastSaccharomycescerevisiaeand requires the emission of trimethylamine (TMA), a pH-raising volatile compound. We show here that TMA emission also profoundly alters the environment around exploring cultures. It specifically reduces iron availability, and this in turn adversely affects the viability of surrounding microbes. Paradoxically,Streptomycesbacteria thrive in these iron-depleted niches, both rewiring their gene expression and metabolism to facilitate iron uptake and increasing their exploration rate. Growth in close proximity to other microbes adept at iron uptake also enhances exploration. Collectively, the data from this work reveal a new role for bacterial volatile compounds in modulating nutrient availability and microbial community behavior. The results further expand the repertoire of interspecies interactions and nutrient cues that impactStreptomycesexploration and provide new mechanistic insight into this unique mode of bacterial growth.


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