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Abstract Sepsis is a leading cause of death worldwide, with most patient mortality stemming from lingering immunosuppression in sepsis survivors. This is due in part to immune dysfunction resulting from monocyte exhaustion, a phenotype of reduced antigen presentation, altered CD14/CD16 inflammatory subtypes, and disrupted cytokine production. Whereas previous research demonstrated improved sepsis survival in Ticam2 -/- mice, the contribution of TICAM2 to long-term exhaustion memory remained unknown. Using a cecal slurry injection sepsis model, we monitored the establishment and recovery of monocyte exhaustion in Ticam2 -/- mice. After one week of recovery, we profiled bone marrow and splenic reservoir monocytes in Ticam2 -/- mice and found that, in contrast to the persistent exhaustion observed in wild-type monocytes, Ticam2 -/- monocytes largely resembled healthy controls. To determine the impact of TICAM2 ablation on innate epigenetic memory in sepsis, we measured genome-wide DNA methylation in bone marrow monocytes and found that Ticam2 -/- cells exhibit a unique profile of altered methylation at CEBPE binding sites and regulatory features for key immune genes such as Dmkn and Btg1. Bearing human translational relevance, a case study of time course blood samples collected from a sepsis patient presenting with SIRS and a positive qSOFA revealed a similar effect in human monocytes, which steadily transition into an exhausted memory characterized by a CD38high; CX3CR1low; HLA-DRlow state within four days of hospital admittance. Together, our data reveal the chronic preservation of monocyte exhaustion, partially controlled by TICAM2.

Abstract Double negative T (DNT) cells are a unique subset of CD3 + TCRαβ + T lymphocytes that lack CD4, CD8, or NK1.1 expression and constitute 3–5% of the total T cell population in C57BL/6 mice. They have increasingly gained recognition for their novel roles in the immune system, especially under autoimmune conditions. Conventional machine learning approaches such as principal component analysis have been employed in single-cell RNA sequencing (scRNA-seq) analysis to characterize DNT cells. However, advanced deep learning models such as Single Cell Variational Inference (scVI) have the capability to capture nonlinear gene expression patterns in the sequencing data. In this study, employing the deep learning methodology, we have revealed novel markers for splenic DNT cells in C57BL/6 mice which were validated with flow cytometry analysis. We classified DNT cells into two subgroups, naïve DNT (nDNT) cells differentiated by the expression of Ly6C and activated DNT (aDNT) cells differentiated by the expression of MHC-II. A prior study had predicted elevated expression of CD137/4-1BB encoded by Tnfrsf9 in nDNT cells; however, our analysis predicted and validated that CD137 was a marker for aDNT cells instead of nDNT cells. Innovatively, our data also identified CD30 encoded by Tnfrsf8 and CD153/CD30L encoded by Tnfsf8 as additional markers for aDNT cells. In addition, we classified three subgroups in nDNT cells and two subgroups in aDNT cells. Our scVI analysis suggested, and flow cytometry analysis confirmed, that Ly49G2 encoded by Klra7 was a marker for the nDNT0 subgroup. Importantly, we validated that MHC-II was indeed expressed by a subset of human DNT cells suggesting the presence of a human aDNT population. Furthermore, we found increased expression of CD30, CD153, and CD137 on aDNT cells in MRL/lpr mice compared to those in C57BL/6 mice suggesting potential pathogenic roles of these molecules in autoimmunity. Together, our comprehensive analysis has uncovered and validated novel markers for different subpopulations of DNT cells that can be used in the phenotypic and/or functional characterization of these relatively rare cells in health and disease.

Abstract Despite the re-emergence of the pioneering “Coley’s toxin” concept in anti-cancer immune therapies highlighted by check-point inhibitors and CAR-T approaches, fundamental mechanisms responsible for the immune-enhancing efficacy of low-dose “Coley’s toxin” remain poorly understood. This study examines the novel reprogramming of immune-enhancing neutrophils by super-low dose endotoxin conducive for anti-cancer therapies. Through integrated analyses including scRNAseq and functional characterizations, we examined the efficacy of reprogrammed neutrophils in treating experimental cancer. We observed that neutrophils trained by super-low dose endotoxin adopt a potent immune-enhancing phenotype characterized by CD177loCD11bloCD80hiCD40hiDectin2hi. Both murine and human neutrophils trained by super-low dose endotoxin exhibit relieved suppression of adaptive T cells as compared to un-trained neutrophils. Functionally, neutrophils trained by super-low dose endotoxin can potently reduce tumor burden when transfused into recipient tumor-bearing mice. Mechanistically, Super-low dose endotoxin enables the generation of immune-enhancing neutrophils through activating STAT5 and reducing innate suppressor IRAK-M. Together, our data clarify the long-held mystery of “Coley’s toxin” in rejuvenating anti-tumor immune defense, and provide a proof-of-concept in developing innate neutrophil-based anti-tumor therapeutics.

Summary: Systemic neutrophil dysregulation contributes to atherosclerosis pathogenesis, and restoring neutrophil homeostasis may be beneficial for treating atherosclerosis. Herein, we report that a homeostatic resolving subset of neutrophils exists in mice and humans characterized by the low expression of TRAM, correlated with reduced expression of inflammatory mediators (leukotriene B4 [LTB4] and elastase) and elevated expression of anti-inflammatory resolving mediators (resolvin D1 [RvD1] and CD200R). TRAM-deficient neutrophils can potently improve vascular integrity and suppress atherosclerosis pathogenesis when adoptively transfused into recipient atherosclerotic animals. Mechanistically, we show that TRAM deficiency correlates with reduced expression of 5-lipoxygenase (LOX5) activating protein (LOX5AP), dislodges nuclear localization of LOX5, and switches the lipid mediator secretion from pro-inflammatory LTB4 to pro-resolving RvD1. TRAM also serves as a stress sensor of oxidized low-density lipoprotein (oxLDL) and/or free cholesterol and triggers inflammatory signaling processes that facilitate elastase release. Together, our study defines a unique neutrophil population characterized by reduced TRAM, capable of homeostatic resolution and treatment of atherosclerosis.

Summary: Monocytes can develop an exhausted memory state characterized by reduced differentiation, pathogenic inflammation, and immune suppression that drives immune dysregulation during sepsis. Chromatin alterations, notably via histone modifications, underlie innate immune memory, but the contribution of DNA methylation remains poorly understood. Using an ex vivo sepsis model, we show altered DNA methylation throughout the genome of exhausted monocytes, including genes implicated in immune dysregulation during sepsis and COVID-19 infection (e.g., Plac8). These changes are recapitulated in septic mice induced by cecal slurry injection. Methylation profiles developed in septic mice are maintained during ex vivo culture, supporting the involvement of DNA methylation in stable monocyte exhaustion memory. Methylome reprogramming is driven in part by Wnt signaling inhibition in exhausted monocytes and can be reversed with DNA methyltransferase inhibitors, Wnt agonists, or immune training molecules. Our study demonstrates the significance of altered DNA methylation in the maintenance of stable monocyte exhaustion memory.

Summary: Monocyte exhaustion with sustained pathogenic inflammation and immune-suppression, a hallmark of sepsis resulting from systemic infections, presents a challenge with limited therapeutic solutions. This study identified Methoxy-Mycolic Acid (M-MA), a branched mycolic acid derived from Mycobacterium bovis Bacillus Calmette–Guérin (BCG), as a potent agent in alleviating monocyte exhaustion and restoring immune homeostasis. Co-treatment of monocytes with M-MA effectively blocked the expansion of Ly6Chi/CD38hi/PD-L1hi monocytes induced by LPS challenges and restored the expression of immune-enhancing CD86. M-MA treatment restored mitochondrial functions of exhausted monocytes and alleviated their suppressive activities on co-cultured T cells. Independent of TREM2, M-MA blocks Src-STAT1-mediated inflammatory polarization and reduces the production of immune suppressors TAX1BP1 and PLAC8. Whole genome methylation analyses revealed M-MA’s ability to erase the methylation memory of exhausted monocytes, particularly restoring Plac8 methylation. Together, our data suggest M-MA as an effective agent in restoring monocyte homeostasis with a therapeutic potential for treating sepsis.

Toll-interacting protein (Tollip) is a negative regulator of the pro-inflammatory response to viruses, including influenza A virus (IAV). Genetic variation of Tollip has been associated with reduced airway epithelial Tollip expression and poor lung function in patients with asthma. Whether Tollip deficiency exaggerates type 2 inflammation (e.g., eosinophils) and viral infection in asthma remains unclear. We sought to address this critical, but unanswered question by using a Tollip deficient mouse asthma model with IAV infection. Further, we determined the underlying mechanisms by focusing on the role of the ATP/IL-33 signaling axis. Wild-type and Tollip KO mice were intranasally exposed to house dust mite (HDM) and IAV with or without inhibitors for IL-33 (i.e., soluble ST2, an IL-33 decoy receptor) and ATP signaling (i.e., an antagonist of the ATP receptor P2Y13). Tollip deficiency amplified airway type 2 inflammation (eosinophils, IL-5, IL-13 and mucins), and the release of ATP and IL-33. Blocking ATP receptor P2Y13 decreased IL-33 release during IAV infection in HDM-challenged Tollip KO mice. Furthermore, soluble ST2 attenuated airway eosinophilic inflammation in Tollip KO mice treated with HDM and IAV. HDM challenges decreased lung viral load in wild-type mice, but Tollip deficiency reduced the protective effects of HDM challenges on viral load. Our data suggests that during IAV infection, Tollip deficiency amplified type 2 inflammation and delayed viral clearance, in part by promoting ATP signaling and subsequent IL-33 release. Our findings may provide several therapeutic targets, including ATP and IL-33 signaling inhibition for attenuating excessive airway type 2 inflammation in human subjects with Tollip deficiency and IAV infection.

Monocyte exhaustion characterized by immune-suppressive features can develop during sepsis and contribute to adverse patient outcomes. However, molecular mechanisms responsible for the establishment of immune-suppressive monocytes with reduced expression of immune-enhancing mediators such as CD86 during sepsis are not well understood. In this study, we identified that the TLR4 intracellular adaptor TRAM plays a key role in mediating the sustained reduction of CD86 expression on exhausted monocytes and generating an immune-suppressive monocyte state. TRAM contributes to the prolonged suppression of CD86 through inducing TAX1BP1 as well as SARM1, collectively inhibiting Akt and NFκB. TRAM deficient mice are protected from cecal slurry-induced experimental sepsis and retain immune-competent monocytes with CD86 expression. Our data reveal a key molecular circuitry responsible for monocyte exhaustion and provide a viable target for rejuvenating functional monocytes and treating sepsis.

Respiratory influenza A virus (IAV) infection continues to pose significant challenges in healthcare of human diseases including asthma. IAV infection in mice was shown to increase IL-33, a key cytokine in driving airway inflammation in asthma, but how IL-33 is regulated during viral infection remains unclear. We previously found that a genetic mutation in Toll-interacting protein (Tollip) was linked to less airway epithelial Tollip expression, increased neutrophil chemokines, and lower lung function in asthma patients. As Tollip is involved in maintaining mitochondrial function, and mitochondrial stress may contribute to extracellular ATP release and IL-33 secretion, we hypothesized that Tollip downregulates IL-33 secretion via inhibiting ATP release during IAV infection. Wild-type and Tollip knockout (KO) mice were infected with IAV and treated with either an ATP converter apyrase or an IL-33 decoy receptor soluble ST2 (sST2). KO mice significantly lost more body weight and had increased extracellular ATP, IL-33 release, and neutrophilic inflammation. Apyrase treatment reduced extracellular ATP levels, IL-33 release, and neutrophilic inflammation in Tollip KO mice. Excessive lung neutrophilic inflammation in IAV-infected Tollip KO mice was reduced by sST2, which was coupled with less IL-33 release. Our data suggest that Tollip inhibits IAV infection, potentially by inhibiting extracellular ATP release and reducing IL-33 activation and lung inflammation. In addition, sST2 may serve as a potential therapeutic approach to mitigate respiratory viral infection in human subjects with Tollip deficiency.

Abstract Neutrophils are the dominant leukocytes in circulation and the first responders to infection and inflammatory cues. While the roles of neutrophils in driving inflammation have been widely recognized, the contribution of neutrophils in facilitating inflammation resolution is under-studied. Here, through single-cell RNA sequencing analysis, we identified a subpopulation of neutrophils exhibiting pro-resolving characteristics with greater Cd200r and Cd86 expression at the resting state. We further discovered that 4-PBA, a peroxisomal stress-reducing agent, can potently train neutrophils into the resolving state with enhanced expression of CD200R, CD86, as well as soluble pro-resolving mediators Resolvin D1 and SerpinB1. Resolving neutrophils trained by 4-PBA manifest enhanced phagocytosis and bacterial-killing functions. Mechanistically, the generation of resolving neutrophils is mediated by the PPARγ/LMO4/STAT3 signaling circuit modulated by TLR4 adaptor molecule TRAM. We further demonstrated that genetic deletion of TRAM renders the constitutive expansion of resolving neutrophils, with an enhanced signaling circuitry of PPARγ/LMO4/STAT3. These findings may have profound implications for the effective training of resolving neutrophils with therapeutic potential in the treatment of both acute infection as well as chronic inflammatory diseases.

Lynette Naler and Yuan-Pang Hsieh et al. evaluate epigenomic and transcriptomic differences in mouse bone marrow-derived macrophages following exposure to high or low doses of LPS. Their results suggest that both low- and high-grade inflammation involve TRAM-dependent pathways.

The Beijing and Zhangjiakou-Bohai Fault Zone is a group of NW-W orderly active fault zones with high seismic activity and abundant geothermal resources since the Cenozoic. Many violent earthquakes occurred here, where it was an important area for earthquake monitoring and research. In order to explore the temporal and spatial variation characteristics of gas geochemistry in the Zhangjiakou-Bohai Fault Zone of the capital circle, this study cited the previous two-stage survey data of 23 geothermal hot springs in the west and east of the Zhangjiakou-Bohai Fault Zone of the capital circle in 2013 and 2018. In order to fill the gap in hot spring gas geochemistry in Beijing (the middle of the Zhangjiakou-Bohai Fault Zone), 21 emergent gas samples from hot springs were collected after many field surveys from October 2020 to November 2021. The test results of 44 gas samples with chemical compositions and isotope changes of helium, neon, and carbon showed that: (1) The helium isotope ratio (3He/4He (Rc/Ra)) of hot spring gases in the Zhangjiakou-Bohai Fault Zone ranged between 0.03 and 2.86Ra (Ra = air, 3He/4He = 1.39 × 10−6), and the calculated maximum proportion of mantle-derived helium was up to 35.4%. It was revealed that although the geological fluid in the fault zone mainly came from crustal source, the mantle-derived helium was still considerable. The hot spring gases in Beijing (the middle of the Zhangjiakou-Bohai Fault Zone) were mainly composed of nitrogen, whose concentration was more than 69%, featuring a low CO2 concentration of 0–6.1% and a δ13CCO2 value ranging from −19‰ to −9.6‰ (vs.PDB) and showing the mixing characteristics of organic sediments and mantle sources. (2) The upwelling release of mantle-derived materials in Zhangjiakou-Bohai Fault Zone shared a good corresponding relationship with regional seismicity, which could promote the inoculation and occurrence of regional earthquakes. In the peak area, the transition zone from the western mountainous area of the Zhangjiakou-Bohai Fault Zone to the plain showed that more mantle-derived materials upwelled, and more deep fluid upwelled. The comparative analysis of regional seismicity showed that deep fluid played an important role in controlling regional seismicity in the area with relatively strong upwelling of deep fluid in the Zhangjiakou-Bohai Fault Zone.

Immune checkpoint blockade antibodies have promising clinical applications, but suffer from severe toxicities and moderate response rates. Here the authors present an electrode-embedded, implantable optical fiber device with both local delivery and tumor impedance measurement capabilities to safely elicit durable anti-tumor immunity.

Deeply-sourced volatiles are releasing from orogenic plateau regions, providing windows to plateau growth dynamics occurring at variable depths. Here the authors show that mantle-derived volatiles reveal the involvement of mantle dynamics in southeastward growth of the Tibetan Plateau.

This data article presents four experimental sets of results related to flax fibre composites with epoxy shape memory polymer matrix: water vapor absorption, mass diffusion immersed in water, hygroscopic expansion, mechanical properties. The water vapor absorption tests are described in raw data related to four types of laminates with weights measured at different relative humidity (0%, 9%, 33%, 44%,75%, 85% and 100%). The mass diffusion experiments are related to weights of immersed samples over time. The unidirectional composite hygroscopic expansion is also measured along the fibre longitude and transverse directions. The mechanical properties of flax composite at various temperatures (20°C, 40°C, 60°C, 80°C and 100°C) and humidity environments (50% and immersed) are also described. Load-displacement diagrams of the hygromorph composites are converted into stress-strain diagrams via a compliance calibration, from which the tensile moduli are extracted. The data presented in this article can provide a benchmark for the development of new models, or for the determination of other properties via post processing. The detailed interpretation of the data can be found in [1]. The data is available in the Mendeley Data repository at [2].

To reveal the heat source and its formation mechanism of the northern Yadong-Gulu rift (YGR), we analyzed the helium isotope, carbon isotope (δ13CCO2), and CO2/3He and CH4/3He ratios of hot spring gases for tracing the source of volatiles and discussing their geological significance. The results show the following: helium is mainly derived from the crust, and the radioactive decay of the thicker crust and granites provided more 4He to the low helium isotopes; thermal decomposition of carbonate rocks is the main source of CO2; CH4 may be of organic origin. To sum up, the gas geochemical characteristics of hot springs in the northern YGR indicate that the volatiles are mainly derived from the crust. The crust/mantle heat flow ratios (qc/qm) calculated by helium isotopes cover a range of 0.84–1.48, suggesting that the heat is mainly contributed by the crust. The crustal origin gas and heat flow demonstrates that the heat source beneath the northern YGR is formed by the process of interior crust. Combined with geophysical data, we suggest that the stress heat caused by the collision of the Indo-Eurasian plate and the radiant heating of the crust lead to the heat source (partial melting) and provide heat for thermal activities.

Hot springs and igneous rocks are present widely in southeast China, influenced by the subduction of the Western Pacific and Philippine Sea Plates. This study reports on new data of chemical compositions and He–Ne–C isotopes for gas samples from representative hot springs and wells in the Guangdong and Fujian provinces to identify the origin of hydrothermal volatiles and provide insight into geothermal tectonic affinities. The primary hydrothermal volatile component from southeast China is atmospheric N2, with a volumetric percentage of 82.19%–98.29%. It indicates medium-low temperature geothermal systems where geothermal fluids suffered a shallow circulation in closed fracture systems. Low CO2 and CH4 contents and their depleted δ13C values confirmed the small number of deep-derived components in the study area. However, spatially discernible geochemical characteristics imply enhanced hydrothermal fluid convection in the adjacent area of the two provinces, including the Fengshun, Zhangzhou, Longyan, and Sanming geothermal fields. Specifically, the He–Ne isotopes from this area exhibit mantle He contribution of more than 10% and mantle heat flow accounts for more than half of the total heat flow. Moreover, according to the thermal background calculations, the highest heat flow value of 77.7 mW/m2 is indicated for the Zhangzhou geothermal area and the lowest value of 54.7 mW/m2 is indicated for the Maoming geothermal area. Given the epicenter distributions and the corresponding earthquake magnitudes, the NE-trending faults are heat-control tectonic structures and their intersections with the NW-trending faults provided expedite channels for geothermal fluids rising to the surface. Therefore, the preferred development potential of geothermal resources can be expected in the adjacent area of the two provinces where two sets of active faults crossed. This study provides critical information on understanding the geothermal distribution controlled by the tectonic structure in southeast China.

Pathogenic inflammation and immuno-suppression are cardinal features of exhausted monocytes increasingly recognized in septic patients and murine models of sepsis. However, underlying mechanisms responsible for the generation of exhausted monocytes have not been addressed. In this report, we examined the generation of exhausted primary murine monocytes through prolonged and repetitive challenges with high dose bacterial endotoxin lipopolysaccharide (LPS). We demonstrated that repetitive LPS challenges skew monocytes into the classically exhausted Ly6Chi population, and deplete the homeostatic non-classical Ly6Clo population, reminiscent of monocyte exhaustion in septic patients. scRNAseq analyses confirmed the expansion of Ly6Chi monocyte cluster, with elevation of pathogenic inflammatory genes previously observed in human septic patients. Furthermore, we identified CD38 as an inflammatory mediator of exhausted monocytes, associated with a drastic depletion of cellular NAD+; elevation of ROS; and compromise of mitochondria respiration, representative of septic monocytes. Mechanistically, we revealed that STAT1 is robustly elevated and sustained in LPS-exhausted monocytes, dependent upon the TRAM adaptor of the TLR4 pathway. TRAM deficient monocytes are largely resistant to LPS-mediated exhaustion, and retain the non-classical homeostatic features. Together, our current study addresses an important yet less-examined area of monocyte exhaustion, by providing phenotypic and mechanistic insights regarding the generation of exhausted monocytes.

Polarization of low-grade inflammatory monocytes facilitates the pathogenesis of atherosclerosis. However, underlying mechanisms as well as approaches for resolving monocyte polarization conducive to the regression of atherosclerosis are not well established. In this report, we demonstrate that TRIF-related adaptor molecule (TRAM) mediated monocyte polarization in vivo and in vitro. TRAM controlled monocyte polarization through activating Src family kinase c-SRC, which not only induces STAT1/STAT5-regulated inflammatory mediators CCR2 and SIRP-α but also suppresses PPARγ-regulated resolving mediator CD200R. Enhanced PPARγ and Pex5 due to TRAM deficiency facilitated peroxisome homeostasis and reduction of cellular reactive oxygen species, further contributing to the establishment of a resolving monocyte phenotype. TRAM-deficient monocytes propagated the resolving phenotype to neighboring monocytes through CD200R-mediated intercellular communication. At the translational level, we show that TRAM-deficient mice were resistant to high-fat diet–induced pathogenesis of atherosclerosis. We further document that intravenous transfusion of TRAM-deficient resolving monocytes into atherosclerotic mice potently reduced the progression of atherosclerosis. Together, our data reveal that targeting TRAM may facilitate the effective generation of resolving monocytes conducive for the treatment of atherosclerosis.

It is unclear why neuronal activity induced methylation changes are limited to specific loci in the genome. Here, authors show that the DNA demethylation enzyme, TET1, gains its specificity via the interaction with EGR1, a sequence specific DNA binding protein.

Abstract The peripheral immune system is a major regulator of the pathophysiology associated with traumatic brain injury (TBI). While age-at-injury influences recovery from TBI, the differential effects on the peripheral immune response remain unknown. Here, we investigated the effects of TBI on gene expression changes in murine whole blood using RNAseq analysis, gene ontology and network topology-based key driver analysis. Genome-wide comparison of CCI-injured peripheral whole blood showed a significant increase in genes involved in proteolysis and oxidative-reduction processes in juvenile compared to adult. Conversely, a greater number of genes, involved in migration, cytokine-mediated signaling and adhesion, were found reduced in CCI-injured juvenile compared to CCI-injured adult immune cells. Key driver analysis also identified G-protein coupled and novel pattern recognition receptor (PRR), P2RY10, as a central regulator of these genes. Lastly, we found Dectin-1, a c-type lectin PRR to be reduced at the protein level in both naïve neutrophils and on infiltrating immune cells in the CCI-injured juvenile cortex. These findings demonstrate a distinct peripheral inflammatory profile in juvenile mice, which may impact the injury and repair response to brain trauma.

Subclinical doses of LPS (SD-LPS) are known to cause low-grade inflammatory activation of monocytes, which could lead to inflammatory diseases including atherosclerosis and metabolic syndrome. Sodium 4-phenylbutyrate is a potential therapeutic compound which can reduce the inflammation caused by SD-LPS. To understand the gene regulatory networks of these processes, we have generated scRNA-seq data from mouse monocytes treated with these compounds and identified 11 novel cell clusters. We have developed a machine learning method to integrate scRNA-seq, ATAC-seq, and binding motifs to characterize gene regulatory networks underlying these cell clusters. Using guided regularized random forest and feature selection, our method achieved high performance and outperformed a traditional enrichment-based method in selecting candidate regulatory genes. Our method is particularly efficient in selecting a few candidate genes to explain observed expression pattern. In particular, among 531 candidate TFs, our method achieves an auROC of 0.961 with only 10 motifs. Finally, we found two novel subpopulations of monocyte cells in response to SD-LPS and we confirmed our analysis using independent flow cytometry experiments. Our results suggest that our new machine learning method can select candidate regulatory genes as potential targets for developing new therapeutics against low grade inflammation.

Subclinical endotoxemia [low levels of bacterial endotoxin (LPS) in the blood stream] has been correlated with chronic inflammatory diseases, with less-understood mechanisms. We have previously shown that chronic exposure to super low doses of LPS polarizes monocytes/macrophages to a pro-inflammatory state characterized by up-regulation of pro-inflammatory regulators such as p62 and simultaneous down-regulation of anti-inflammatory/resolving regulators such as Nrf2. Building upon this observation, here we show that chronic exposure to super-low doses of LPS leads to accumulation of the Nrf2-inhibitory protein Keap1 in murine monocytes. This is accompanied by increases of p62 and MLKL, consistent with a disruption of autolysosome function in polarized monocytes challenged by super-low dose LPS. Monocytes subjected to persistent super-low dose LPS challenge also accumulate higher levels of IKKβ. As a consequence, SLD-LPS challenge leads to an inflammatory monocyte state represented by higher expression of the inflammatory marker Ly6C as well as lower expression of the anti-inflammatory marker CD200R. Further analysis revealed that Keap1 levels are significantly enriched in the Ly6Chi pro-inflammatory monocyte population. Finally, we show that the TLR4 signaling adaptor TRAM is essential for these effects. Together our study provides novel insight into signaling mechanisms behind low-grade inflammatory monocyte polarization unique to chronic super-low dose LPS exposure.

Abstract Background Systemic lupus erythematosus, characterized by persistent inflammation, is a complex autoimmune disorder with no known cure. Immunosuppressants used in treatment put patients at a higher risk of infections. New knowledge of disease modulators, such as symbiotic bacteria, can enable fine-tuning of parts of the immune system, rather than suppressing it altogether. Results Dysbiosis of gut microbiota promotes autoimmune disorders that damage extraintestinal organs. Here we report a role of gut microbiota in the pathogenesis of renal dysfunction in lupus. Using a classical model of lupus nephritis, MRL/lpr, we found a marked depletion of Lactobacillales in the gut microbiota. Increasing Lactobacillales in the gut improved renal function of these mice and prolonged their survival. We used a mixture of 5 Lactobacillus strains (Lactobacillus oris, Lactobacillus rhamnosus, Lactobacillus reuteri, Lactobacillus johnsonii, and Lactobacillus gasseri), but L. reuteri and an uncultured Lactobacillus sp. accounted for most of the observed effects. Further studies revealed that MRL/lpr mice possessed a “leaky” gut, which was reversed by increased Lactobacillus colonization. Lactobacillus treatment contributed to an anti-inflammatory environment by decreasing IL-6 and increasing IL-10 production in the gut. In the circulation, Lactobacillus treatment increased IL-10 and decreased IgG2a that is considered to be a major immune deposit in the kidney of MRL/lpr mice. Inside the kidney, Lactobacillus treatment also skewed the Treg-Th17 balance towards a Treg phenotype. These beneficial effects were present in female and castrated male mice, but not in intact males, suggesting that the gut microbiota controls lupus nephritis in a sex hormone-dependent manner. Conclusions This work demonstrates essential mechanisms on how changes of the gut microbiota regulate lupus-associated immune responses in mice. Future studies are warranted to determine if these results can be replicated in human subjects.

Non-resolving inflammatory monocytes/macrophages are critically involved in the pathogenesis of chronic inflammatory diseases. However, mechanisms of macrophage polarization are not well understood, thus hindering the development of effective strategies to promote inflammation resolution. In this study, we report that macrophages polarized by subclinical super-low dose LPS preferentially expressed pro-inflammatory mediators such as ccl2 (which encodes the protein monocyte chemo attractant protein-1) with reduced expression of anti-inflammatory/homeostatic mediators such as slc40a1 (which encodes the protein ferroportin-1). We observed significantly elevated levels of the autophagy-associated and pro-inflammatory protein p62 in polarized macrophages, closely correlated with the inflammatory activation of ccl2 gene expression. In contrast, we noted a significant increase of ubiquitinated/inactive nuclear-erythroid-related factor 2 (NRF2), consistent with reduced slc40a1 gene expression in polarized macrophages. Addition of the homeostatic restorative agent phenylbutyrate (4-PBA) effectively reduced cellular levels of p62 as well as ccl2 gene induction by super-low dose LPS. On the other hand, application of 4-PBA also blocked the accumulation of ubiquitinated NRF2 and restored anti-inflammatory slc40a1 gene expression in macrophages. Together, our study provides novel insights with regard to macrophage polarization and reveals 4-PBA as a promising molecule in restoring macrophage homeostasis.

Neutrophils are known to adopt dynamic and distinct functional phenotypes involved in the modulation of inflammation and immune homeostasis. However, inter-cellular signaling mechanisms that govern neutrophil polarization dynamics are not well understood. Employing a novel model of PHLPP deficient mice, we examined how neutrophils deficient in PHLPP may uniquely modulate immune defense and the host response during acute colitis. We found that PHLPP−/− mice were protected from dextran sodium sulfate (DSS)-induced septic colitis characterized by minimal body weight-loss, alleviated colon tissue destruction and reduced clinical symptoms. PHLPP−/− neutrophils have enhanced immune homeostasis as compared to WT neutrophils, reflected in enhanced migratory capacity toward chemoattractants, and reduced expression of inflammatory mediators due to elevated phosphorylation of AKT, STAT1, and ERK. Further, adoptive transfer of PHLPP deficient neutrophils to WT mice is sufficient to potently alleviate the severity of DSS-induced colitis. Our data reveal that PHLPP deficient neutrophils can be uniquely reprogrammed to a state conducive to host inflammation resolution. As a consequence, PHLPP−/− neutrophils can effectively transfer immune homeostasis in mice subjected to acute colitis. Our findings hold significant and novel insights into the mechanisms by which neutrophils can be effectively reprogrammed into a homeostatic state conducive for treating acute injuries such as septic colitis.

Neutrophils are the first responders to infection and play a pivotal role in many inflammatory diseases, including sepsis. Recent studies have shown that lipopolysaccharide (LPS), a classical pattern recognition molecule, dynamically programs innate immune responses. In this study, we show that pre-treatment with super-low levels of LPS [1 ng/mL] significantly dysregulate neutrophil migratory phenotypes, including spontaneous migration and altering neutrophil decision-making. To quantify neutrophil migratory decision-making with single-cell resolution, we developed a novel microfluidic competitive chemotaxis-chip (μC3) that exposes cells in a central channel to competing chemoattractant gradients. In this reductionist approach, we use two chemoattractants: a pro-resolution (N-Formyl-Met-Leu-Phe, fMLP) and pro-inflammatory (Leukotriene B4, LTB4) chemoattractant to model how a neutrophil makes a decision to move toward an end target chemoattractant (e.g., bacterial infection) vs. an intermediary chemoattractant (e.g., inflammatory signal). We demonstrate that naïve neutrophils migrate toward the primary end target signal in higher percentages than toward the secondary intermediary signal. As expected, we found that training with high dose LPS [100 ng/mL] influences a higher percentage of neutrophils to migrate toward the end target signal, while reducing the percentage of neutrophils that migrate toward the intermediary signal. Surprisingly, super-low dose LPS [1 ng/mL] significantly changes the ratios of migrating cells and an increased percentage of cells migrate toward the intermediary signal. Significantly, there was also an increase in the numbers of spontaneously migrating neutrophils after treatment with super-low dose LPS. These results shed light onto the directional migratory decision-making of neutrophils exposed to inflammatory training signals. Understanding these mechanisms may lead to the development of pro-resolution therapies that correct the neutrophil compass and reduce off-target organ damage.

Aberrant inflammation is a hallmark of inflammatory bowel disease (IBD) and colorectal cancer. IRAK-M is a critical negative regulator of TLR signaling and overzealous inflammation. Here we utilize data from human studies and Irak-m−/− mice to elucidate the role of IRAK-M in the modulation of gastrointestinal immune system homeostasis. In human patients, IRAK-M expression is up-regulated during IBD and colorectal cancer. Further functional studies in mice revealed that Irak-m−/− animals are protected against colitis and colitis associated tumorigenesis. Mechanistically, our data revealed that the gastrointestinal immune system of Irak-m−/− mice is highly efficient at eliminating microbial translocation following epithelial barrier damage. This attenuation of pathogenesis is associated with expanded areas of gastrointestinal associated lymphoid tissue (GALT), increased neutrophil migration, and enhanced T-cell recruitment. Further evaluation of Irak-m−/− mice revealed a splice variant that robustly activates NF-κB signaling. Together, these data identify IRAK-M as a potential target for future therapeutic intervention.

A new method had been developed for the analysis of hydrogen isotopic composition of trace hydrocarbons in natural gas samples by using solid phase microextraction (SPME) combined with gas chromatography-isotope ratio mass spectrometry (GC/IRMS). In this study, the SPME technique had been initially introduced to achieve the enrichment of trace content of hydrocarbons with low abundance and coupled to GC/IRMS for hydrogen isotopic analysis. The main parameters, including the equilibration time, extraction temperature, and the fiber type, were systematically optimized. The results not only demonstrated that high extraction yield was true but also shows that the hydrogen isotopic fractionation was not observed during the extraction process, when the SPME device fitted with polydimethylsiloxane/divinylbenzene/carbon molecular sieve (PDMS/DVB/CAR) fiber. The applications of SPME-GC/IRMS method were evaluated by using natural gas samples collected from different sedimentary basins; the standard deviation (SD) was better than 4‰ for reproducible measurements; and also, the hydrogen isotope values from C1 to C9 can be obtained with satisfying repeatability. The SPME-GC/IRMS method fitted with PDMS/DVB/CAR fiber is well suited for the preconcentration of trace hydrocarbons, and provides a reliable hydrogen isotopic analysis for trace hydrocarbons in natural gas samples.

Chronic low-grade inflammation has been suspected to promote atherosclerosis. Here, Geng et al. show that sustained low-grade inflammation promotes atherosclerosis in mice via monocyte programing that involves a coupled disruption of IRAK-M regulation and induction of miR-24.

Gas geochemical analysis was conducted on the shale gas from the Longmaxi Formation in the Weiyuan-Changning areas, Sichuan Basin, China. Chemical composition was measured using an integrated method of gas chromatography combined with mass spectrometry. The results show that the Longmaxi shale gas, after hydraulic fracturing, is primarily dominated by methane (94.0%–98.6%) with low humidity (0.3%–0.6%) and minor non-hydrocarbon gasses which are primarily comprised of CO2, N2, as well as trace He. δ13CCO2 = −2.5‰−6.0‰3He/4He = 0.01–0.03Ra.The shale gas in the Weiyuan and Changning areas display carbon isotopes reversal pattern with a carbon number (δ13C1 > δ13C2) and distinct carbon isotopic composition. The shale gas from the Weiyuan pilot has heavier carbon isotopic compositions for methane (δ13C1: from −34.5‰ to −36.8‰), ethane (δ13C2: −37.6‰ to −41.9‰), and CO2 (δ13CCO2: −4.5‰ to −6.0‰) than those in the Changning pilot (δ13C1: −27.2‰ to −27.3‰, δ13C2: −33.7‰ to −34.1‰, δ13CCO2: −2.5‰ to −4.6‰). The Longmaxi shale was thermally high and the organic matter was in over mature stage with good sealing conditions. The shale gas, after hydraulic fracturing, could possibly originate from the thermal decomposition of kerogen and the secondary cracking of liquid hydrocarbons which caused the reversal pattern of carbon isotopes. Some CO2 could be derived from the decomposition of carbonate. The difference in carbon isotopes between the Weiyuan and Changning areas could be derived from the different mixing proportion of gas from the secondary cracking of liquid hydrocarbons caused by specific geological and geochemical conditions.

The Weiyuan (WY) and Changning (CN) fields are the largest shale gas fields in the Sichuan Basin. Though the shale gases in both fields are sourced from the Longmaxi Formation, this study found notable differences between them in molecular composition, carbon isotopic composition, and noble gas abundance and isotopic composition. CO2 (av. 0.52%) and N2 (av. 0.94%) were higher in Weiyuan than in Changning by an average of 0.45% and 0.70%, respectively. The δ13C1 (−26.9% to −29.7%) and δ13C2 (−32.0% to −34.9%) ratios in the Changning shale gases were about 8% and 6% heavier than those in Weiyuan, respectively. Both shale gases had similar 3He/4He ratios but different 40Ar/36Ar ratios. These geochemical differences indicated complex geological conditions and shed light on the evolution of the Lonmaxi shale gas in the Sichuan Basin. In this study, we highlight the possible impacts on the geochemical characteristics of gas due to tectonic activity, thermal evolution, and migration. By combining previous gas geochemical data and the geological background of these natural gas fields, we concluded that four factors account for the differences in the Longmaxi Formation shale gas in the Sichuan Basin: a) A different ratio of oil cracking gas and kerogen cracking gas mixed in the closed system at the high over-mature stage. b) The Longmaxi shales in WY and CN have had differential geothermal histories, especially in terms of the effects from the Emeishan Large Igneous Province (LIP), which have led to the discrepancy in evolution of the shales in the two areas. c) The heterogeneity of the Lower Silurian Longmaxi shales is another important factor, according to the noble gas data. d) Although shale gas is generated in closed systems, natural gas loss throughout geological history cannot be avoided, which also accounts for gas geochemical differences. This research offers some useful information regarding the theory of shale gas generation and evolution.

The Podong Permian ultramafic intrusion is only one ultramafic intrusion with massif Ni-Cu sulfide mineralization in the Pobei layered mafic-ultramafic complex, western China. It is obviously different in sulfide mineralization from the nearby coeval Poyi ultramafic intrusion with the largest disseminated Ni-Cu sulfide mineralization and mantle plume contribution (Zhang et al., 2017). The type and addition mechanism of the confirmed crustal contaminations and possible mantle plume involved in the intrusion formation require evidences from carbon and noble gas isotopic compositions. In the present study, we have measured C, He, Ne, and Ar isotopic compositions of volatiles from magmatic minerals in the Podong ultramafic intrusion. The results show that olivine, pyroxene, and plagioclase minerals in the Podong intrusion have variable δ13C of CO2 (-24.5‰ to -3.2‰). The CH4, C2H6, C3H8, and C4H10 hydrocarbon gases show normal or partial reversal distribution patterns of carbon isotope with carbon number and light δ13C1 value of CH4, indicating the hydrocarbon gases of biogenic origin. The δ13C of CO2 and CH4 suggested the magmatic volatile of the mantle mixed with the volatiles of thermogenic and crustal origins. Carbon and noble gas isotopes indicated that the Podong intrusion could have a different petrogenesis from the Poyi ultramafic intrusion. Two types of contaminated crustal materials can be identified as crustal fluids from subducted altered oceanic crust (AOC) in the lithospheric mantle source and a part of the siliceous crust. The carbon isotopes for different minerals show that magma spent some time crystallizing in a magma chamber during which assimilation of crustal material occurred. Subduction-devolatilization of altered oceanic crust could be the best mechanism that transported large proportion of ASF (air-saturated fluid) and crustal components into the mantle source. The mantle plume existing beneath the Poyi intrusion could provide less contribution of real materials of silicate and fluid components.

A series of samples including natural gas, formation water, and rocks were collected from volcanic rock reservoirs in the Niudong area of the Santanghu Oilfields and analyzed for their mineral and/or chemical compositions and sulfur and carbon isotopes in order to investigate the occurrence and origin of hydrogen sulfide (H2S). H2S was mostly dissolved in the formation water along with petroleum production in the study area. The δ34S values of on-well H2S samples varied in a range of 9.2‰ to 20.5‰, probably indicating thermochemical sulfate reduction (TSR) and/or thermal decomposition of organic sulfur-bearing compounds (TDS) as the genetic process for H2S. However, the chemical composition of formation waters from the Kalagang Formation (C2k) and their coefficient of desulfurization also revealed that TSR could be the main principle for H2S formation. Considering the regional geological background, especially the tectonic structures and thermal evolution features of the basin, it was concluded that H2S in the study area was dominantly produced by thermal genesis with TSR as a domain through interactions between hydrocarbons and aqueous sulfate dissolved from sulfate minerals.

Chronic cigarette smoking is widely known to alter immune functions and compromise host defense against microbial infection. Neutrophils play an essential role in the immune defense against microbial pathogens and also participate in the development of the inflammatory responses. However, there is limited information about the effects of cigarette smoking on neutrophil response. In this study, cultured bone marrow neutrophils were exposed to total particulate matter (TPM) from cigarette smoke. We found that TPM not only reduced LPS-induced TNFα production, but also suppressed neutrophil bactericidal activity. We also observed that TPM priming reduced the expression of NADPH oxidase component gp91 and iNOS, molecules important for bacterial killing. Mechanistically, we documented that TPM-primed neutrophils have reduced STAT1 activation following subsequent LPS challenge. STAT1 is a key transcription factor responsible for the expression of inflammatory genes as well as gp91 and iNOS. Collectively, reduced STAT1 activation and reduced NADPH oxidase/iNOS may potentially explain the compromised anti-microbial function of TPM-programmed neutrophils. Taken together, our findings reveal that the key innate immune neutrophil is subject to reprogramming by smoking to adopt an immune-suppressed state, potentially responsible for chronic smoking-mediated immunosuppression.

Granulocyte-monocyte progenitor (GMP) cells play a vital role in the immune system by maturing into a variety of white blood cells, including neutrophils and macrophages, depending on exposure to cytokines such as various types of colony stimulating factors (CSF). Granulocyte-CSF (G-CSF) induces granulopoiesis and macrophage-CSF (M-CSF) induces monopoiesis, while granulocyte/macrophage-CSF (GM-CSF) favors monocytic and granulocytic differentiation at low and high concentrations, respectively. Although these differentiation pathways are well documented, the mechanisms behind the diverse behavioral responses of GMP cells to CSFs are not well understood. In this paper, we propose a mechanism of interacting CSF-receptors and transcription factors that control GMP differentiation, convert the mechanism into a set of differential equations, and explore the properties of this mathematical model using dynamical systems theory. Our model reproduces numerous experimental observations of GMP cell differentiation in response to varying dosages of G-CSF, M-CSF, and GM-CSF. In particular, we are able to reproduce the concentration-dependent behavior of GM-CSF induced differentiation, and propose a mechanism driving this behavior. In addition, we explore the differentiation of a fourth phenotype, monocytic myeloid-derived suppressor cells (M-MDSC), showing how they might fit into the classical pathways of GMP differentiation and how progenitor cells can be primed for M-MDSC differentiation. Finally, we use the model to make novel predictions that can be explored by future experimental studies.

Allergens are molecules that elicit a hypersensitive inflammatory response in sensitized individuals and are derived from a variety of sources. Alt a 1 is the most clinically important secreted allergen of the ubiquitous fungus, Alternaria. It has been shown to be a major allergen causing IgE-mediated allergic response in the vast majority of Alternaria-sensitized individuals. However, no studies have been conducted in regards to the innate immune eliciting activities of this clinically relevant protein. In this study, recombinant Alt a 1 was produced, purified, labeled, and incubated with BEAS-2B, NHBE, and DHBE human lung epithelial cells. Alt a 1 elicited strong induction of IL-8, MCP-1, and Gro-a/b/g. Using gene-specific siRNAs, blocking antibodies, and chemical inhibitors such as LPS-RS, it was determined that Alt a 1-induced immune responses were dependent upon toll-like receptors (TLRs) 2 and 4, and the adaptor proteins MYD88 and TIRAP. Studies utilizing human embryonic kidney cells engineered to express single receptors on the cell surface such as TLRs, further confirmed that Alt a 1-induced innate immunity is dependent upon TLR4 and to a lesser extent TLR2.

Sepsis mortality varies dramatically in individuals of variable immune conditions, with poorly defined mechanisms. This phenomenon complements the hypothesis that innate immunity may adopt rudimentary memory, as demonstrated in vitro with endotoxin priming and tolerance in cultured monocytes. However, previous in vivo studies only examined the protective effect of endotoxin tolerance in the context of sepsis. In sharp contrast, we report herein that pre-conditioning with super-low or low dose endotoxin lipopolysaccharide (LPS) cause strikingly opposite survival outcomes. Mice pre-conditioned with super-low dose LPS experienced severe tissue damage, inflammation, increased bacterial load in circulation, and elevated mortality when they were subjected to cecal-ligation and puncture (CLP). This is in contrast to the well-reported protective phenomenon with CLP mice pre-conditioned with low dose LPS. Mechanistically, we demonstrated that super-low and low dose LPS differentially modulate the formation of neutrophil extracellular trap (NET) in neutrophils. Instead of increased ERK activation and NET formation in neutrophils pre-conditioned with low dose LPS, we observed significantly reduced ERK activation and compromised NET generation in neutrophils pre-conditioned with super-low dose LPS. Collectively, our findings reveal a mechanism potentially responsible for the dynamic programming of innate immunity in vivo as it relates to sepsis risks.

Solid-phase microextraction (SPME) coupled with gas chromatography-isotope ratio mass spectrometry (GC-IRMS) has already been applied to collect and identify volatile light hydrocarbons in oil and source rocks. However, this technology has not yet been used to analyze volatile light hydrocarbons in dry gas (natural gas with C1/C2+ > 95%). In this study, we developed a method to measure the molecular and carbon isotope composition of natural gas using divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS) fiber. This fiber proved to be suitable for extracting C1–C9 hydrocarbons from natural gas without inducing carbon isotopic fractionation. Notably, the extraction coefficients of the analytes were not the same but rather increased with the increasing carbon number of the hydrocarbons. Nevertheless, we successfully identified 24 hydrocarbons from the in-lab standard natural gas, while also obtaining the carbon isotope composition of C1 to C9 hydrocarbons with satisfying repeatability. The relative standard deviation (RSD) of the molecular composition data was in the range of 0.06–0.74%, with the RSDs of the carbon isotope composition data not exceeding 1‰. Finally, seven natural gas samples, collected from different sedimentary basins, were successfully analyzed and the stable carbon isotope compositions of C1–C9 hydrocarbons present in these were determined through this method. Overall, the new approach provides a simple but useful technique to obtain more geochemical information about the source and evolution of natural gas.

Innate leukocytes manifest dynamic and distinct inflammatory responses upon challenges with rising dosages of pathogen-associated molecular pattern molecules such as lipopolysaccharide (LPS). To differentiate signal strengths, innate leukocytes may utilize distinct intracellular signaling circuitries modulated by adaptor molecules. Toll-interacting protein (Tollip) is one of the critical adaptor molecules potentially playing key roles in modulating the dynamic adaptation of innate leukocytes to varying dosages of external stimulants. While Tollip may serve as a negative regulator of nuclear factor κ of activated B cells signaling pathway in cells challenged with higher dosages of LPS, it acts as a positive regulator for low-grade chronic inflammation in leukocytes programmed by subclinical low-dosages of LPS. This review aims to discuss recent progress in our understanding of complex innate leukocyte dynamics and its relevance in the pathogenesis of resolving versus non-resolving chronic inflammatory diseases.

BackgroundCompromised lipophagy with unknown mechanisms may be critically involved in the intracellular accumulation of lipids, contributing to elevated atherosclerosis and liver steatosis. We hypothesize that toll‐interacting protein (Tollip), a key innate immune molecule involved in the fusion of autolysosome, may play a significant role in lipophagy and modulate lipid accumulation during the pathogenesis of atherosclerosis and liver steatosis. Methods and ResultsBy comparing mice fed with either a Western high‐fat diet or a regular chow diet, we observed that both atherosclerosis and liver steatosis were aggravated in apolipoprotein E–deficient (ApoE−/−)/Tollip−/− mice as compared with ApoE−/− mice. Through electron microscopy analyses, we observed compromised fusion of lipid droplets with lysosomes within aortic macrophages as well as liver hepatocytes from ApoE−/−/Tollip−/− mice as compared with ApoE−/− mice. As a molecular indicator for disrupted lysosome fusion, the levels of p62 were significantly elevated in aortic and liver tissues from ApoE−/−/Tollip−/− mice. Molecules involved in facilitating lipophagy completion such as Ras‐related protein 7 and gamma‐aminobutyric acid receptor‐associated protein were reduced in ApoE−/−/Tollip−/− mice as compared with ApoE−/− mice. Intriguingly, ApoE−/−/Tollip−/− mice had reduced circulating levels of inflammatory cytokines such as tumor necrosis factor‐α and increased levels of transforming growth factor‐β. The reduced inflammation due to Tollip deficiency is consistent with a stable atherosclerotic plaque phenotype with increased levels of plaque collagen and smooth muscle cells in ApoE−/−/Tollip−/− mice. ConclusionsTollip deficiency selectively leads to enlarged yet stable atherosclerotic plaques, increased circulating lipids, liver steatosis, and reduced inflammation. Compromised lipophagy and reduced expression of inflammatory mediators due to Tollip deficiency may be the underlying causes. Our data suggest that lipid accumulation and inflammation may be intertwined yet independent processes during the progression of atherosclerosis and steatosis.

In adaptation to rising stimulant strength, innate monocytes can be dynamically programmed to preferentially express either pro- or anti-inflammatory mediators. Such dynamic innate adaptation or programming may bear profound relevance in host health and disease. However, molecular mechanisms that govern innate adaptation to varying strength of stimulants are not well understood. Using lipopolysaccharide (LPS), the model stimulant of Toll-Like-Receptor 4 (TLR4), we reported that the expressions of pro-inflammatory mediators are preferentially sustained in monocytes adapted by lower doses of LPS, and suppressed/tolerized in monocytes adapted by higher doses of LPS. Mechanistically, monocytes adapted by super-low dose LPS exhibited higher levels of transcription factor IRF5 and reduced levels of transcriptional modulator BLIMP-1. Intriguingly, the inflammatory monocyte adaptation by super-low dose LPS is dependent upon TRAM/TRIF but not MyD88. Similar to LPS, we also observed biphasic inflammatory adaptation and tolerance in monocytes challenged with varying dosages of TLR7 agonist. In sharp contrast, rising doses of TLR3 agonist preferentially caused inflammatory adaptation without inducing tolerance. At the molecular level, the differential regulation of IRF5 and Blimp-1 coincides with unique monocyte adaptation dynamics by TLR4/7 and TLR3 agonists. Our study provides novel clue toward the understanding of monocyte adaptation and memory toward distinct TLR ligands.

Human rhinovirus (HRV) is the most common cause of acute exacerbations of chronic lung diseases including asthma. Impaired anti-viral IFN-λ1 production and increased HRV replication in human asthmatic airway epithelial cells may be one of the underlying mechanisms leading to asthma exacerbations. Increased autophagy has been shown in asthmatic airway epithelium, but the role of autophagy in anti-HRV response remains uncertain. Trehalose, a natural glucose disaccharide, has been recognized as an effective autophagy inducer in mammalian cells. In the current study, we used trehalose to induce autophagy in normal human primary airway epithelial cells in order to determine if autophagy directly regulates the anti-viral response against HRV. We found that trehalose-induced autophagy significantly impaired IFN-λ1 expression and increased HRV-16 load. Inhibition of autophagy via knockdown of autophagy-related gene 5 (ATG5) effectively rescued the impaired IFN-λ1 expression by trehalose and subsequently reduced HRV-16 load. Mechanistically, ATG5 protein interacted with retinoic acid-inducible gene I (RIG-I) and IFN-β promoter stimulator 1 (IPS-1), two critical molecules involved in the expression of anti-viral interferons. Our results suggest that induction of autophagy in human primary airway epithelial cells inhibits the anti-viral IFN-λ1 expression and facilitates HRV infection. Intervention of excessive autophagy in chronic lung diseases may provide a novel approach to attenuate viral infections and associated disease exacerbations.

The neutrophil gelatinase-associated lipocalin 2 (LCN2) is a critical inflammatory mediator persistently induced during endotoxemia, contributing to tubular damage and kidney failure. The intracellular process responsible for persistent induction of LCN2 by bacterial endotoxin Lipopolysaccharide (LPS) is not well understood. Using primary kidney fibroblasts, we observed that LPS-induced LCN2 expression requires a coupled circuit involving an early transient phase of AP-1 path and a late persistent phase of C/EBPδ path, both of which are dependent upon the interleukin 1 receptor associated kinase 1 (IRAK-1). Using immunoprecipitation analysis we observed transient binding of AP-1 to the promoters of both TNFα and C/ebpδ. On the other hand, we only observed persistent binding of C/EBPδ to its own promoter but not on TNFα. Blockage of new protein synthesis using cyclohexamide significantly reduced the expression of C/EBPδ as well as LCN2. By chromatin immunoprecipitation analyses, we demonstrated that LPS recruited C/EBPδ to the Lcn2 promoter in WT, but not IRAK-1 deficient fibroblasts. A differential equation-based computational model captured the dynamic circuit leading to the persistent induction of LCN2. In vivo, we observed elevated levels of LCN2 in kidneys harvested from LPS-injected WT mice as compared to IRAK-1 deficient mice. Taken together, this study has identified an integrated intracellular network involved in the persistent induction of LCN2 by LPS.

The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are classic examples of the complex adaptation of innate immune cells. Upon repetitive exposures to different doses of bacterial endotoxin (lipopolysaccharide) or other stimulants, macrophages show either suppressed or augmented inflammatory responses compared to a single exposure to the stimulant. Endotoxin tolerance and priming are critically involved in both immune homeostasis and the pathogenesis of diverse inflammatory diseases. However, the underlying molecular mechanisms are not well understood. By means of a computational search through the parameter space of a coarse-grained three-node network with a two-stage Metropolis sampling approach, we enumerated all the network topologies that can generate priming or tolerance. We discovered three major mechanisms for priming (pathway synergy, suppressor deactivation, activator induction) and one for tolerance (inhibitor persistence). These results not only explain existing experimental observations, but also reveal intriguing test scenarios for future experimental studies to clarify mechanisms of endotoxin priming and tolerance.

The reciprocal differentiation of T helper 17 (T(H)17) cells and induced regulatory T (iT(reg)) cells plays a critical role in both the pathogenesis and resolution of diverse human inflammatory diseases. Although initial studies suggested a stable commitment to either the T(H)17 or the iT(reg) lineage, recent results reveal remarkable plasticity and heterogeneity, reflected in the capacity of differentiated effectors cells to be reprogrammed among T(H)17 and iT(reg) lineages and the intriguing phenomenon that a group of naïve precursor CD4(+) T cells can be programmed into phenotypically diverse populations by the same differentiation signal, transforming growth factor beta. To reconcile these observations, we have built a mathematical model of T(H)17/iT(reg) differentiation that exhibits four different stable steady states, governed by pitchfork bifurcations with certain degrees of broken symmetry. According to the model, a group of precursor cells with some small cell-to-cell variability can differentiate into phenotypically distinct subsets of cells, which exhibit distinct levels of the master transcription-factor regulators for the two T cell lineages. A dynamical control system with these properties is flexible enough to be steered down alternative pathways by polarizing signals, such as interleukin-6 and retinoic acid and it may be used by the immune system to generate functionally distinct effector cells in desired fractions in response to a range of differentiation signals. Additionally, the model suggests a quantitative explanation for the phenotype with high expression levels of both master regulators. This phenotype corresponds to a re-stabilized co-expressing state, appearing at a late stage of differentiation, rather than a bipotent precursor state observed under some other circumstances. Our simulations reconcile most published experimental observations and predict novel differentiation states as well as transitions among different phenotypes that have not yet been observed experimentally.

Despite extensive research, the pathogenesis of neurodegenerative Alzheimer's disease (AD) still eludes our comprehension. This is largely due to complex and dynamic cross-talks that occur among multiple cell types throughout the aging process. We present a mathematical model that helps define critical components of AD pathogenesis based on differential rate equations that represent the known cross-talks involving microglia, astroglia, neurons, and amyloid-β (Aβ). We demonstrate that the inflammatory activation of microglia serves as a key node for progressive neurodegeneration. Our analysis reveals that targeting microglia may hold potential promise in the prevention and treatment of AD.

Recent identifications of associations between novel variants in inflammation-related genes and several common diseases emphasize the need for systematic evaluations of these genes in disease susceptibility. Considering that many genes are involved in the complex inflammation responses and many genetic variants in these genes have the potential to alter the functions and expression of these genes, we assembled a list of key inflammation-related genes to facilitate the identification of genetic associations of diseases with an inflammation-related etiology. We first reviewed various phases of inflammation responses, including the development of immune cells, sensing of danger, influx of cells to sites of insult, activation and functional responses of immune and non-immune cells, and resolution of the immune response. Assisted by the Ingenuity Pathway Analysis, we then identified 17 functional sub-pathways that are involved in one or multiple phases. This organization would greatly increase the chance of detecting gene-gene interactions by hierarchical clustering of genes with their functional closeness in a pathway. Finally, as an example application, we have developed tagging single nucleotide polymorphism (tSNP) arrays for populations of European and African descent to capture all the common variants of these key inflammation-related genes. Assays of these tSNPs have been designed and assembled into two Affymetrix ParAllele customized chips, one each for European (12,011 SNPs) and African (21,542 SNPs) populations. These tSNPs have greater coverage for these inflammation-related genes compared to the existing genome-wide arrays, particularly in the African population. These tSNP arrays can facilitate systematic evaluation of inflammation pathways in disease susceptibility. For additional applications, other genotyping platforms could also be employed. For existing genome-wide association data, this list of key inflammation-related genes and associated subpathways can facilitate comprehensive inflammation pathway- focused association analyses.