Rapid proteasomal elimination of 3-hydroxy-3-methylglutaryl-CoA reductase by interferon-γ in primary macrophages requires endogenous 25-hydroxycholesterol synthesis (in press)

AbstractInterferons (IFNs) play a central role in immunity and emerging evidence suggests that IFN-signalling coordinately regulates sterol biosynthesis in macrophages, via Sterol Regulatory Element-Binding Protein (SREBP) dependent and independent pathways. However, the precise mechanisms and kinetic steps by which IFN controls sterol biosynthesis are as yet not fully understood. Here, we elucidate the molecular circuitry governing how IFN controls the first regulated step in the mevalonate-sterol pathway, 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR), through the synthesis of 25-Hydroxycholesterol (25-HC) from cholesterol by the IFN-inducible Cholesterol-25-Hydroxylase (CH25H). We show for the first 30-min of IFN stimulation of macrophages the rate of de novo synthesis of the Ch25h transcript is markedly increased but by 120-min becomes transcriptionally curtailed, coincident with induction of the Activating Transcription Factor 3 (ATF3) repressor. We demonstrate ATF3 induction by Toll-like receptors is strictly dependent on IFN-signalling. While the SREBP-pathway dependent rates of de novo transcription of Hmgcr are relatively unchanged in the first 90-min of IFN treatment, we find HMGCR enzyme levels undergo a rapid proteasomal-mediated degradation, defining a previously unappreciated SREBP-independent mechanism for IFN-action. These events precede a sustained marked reduction in Hmgcr RNA levels involving SREBP-dependent mechanisms. We demonstrate that HMGCR proteasomal-degradation by IFN strictly requires the synthesis of endogenous 25-HC and functionally couples HMGCR to CH25H to coordinately suppress sterol biosynthesis. In conclusion, we quantitatively delineate proteomic and transcriptional levels of IFN-mediated control of HMGCR, the primary enzymatic step of the mevalonate-sterol biosynthesis pathway, providing a foundational framework for mathematically modelling the therapeutic outcome of immune-metabolic pathways

Enhanced Anti-tumor of Pep-1 Modified Superparamagnetic Iron Oxide/PTX Loaded Polymer Nanoparticles

Superparamagnetic iron-oxide nanoparticle (SPION) has gained tremendous attention for drug delivery applications due to their unique properties. In this study, we developed a dual targeted delivery system with paclitaxel (PTX) and SPION co-loaded PLGA nanoparticles, modified with Pep-1 peptide (Pep-NP-SPION/PTX), to achieve magnetic targeting and active targeting for tumor treatment. SPION was synthesized by a co-precipitation method and was then encapsulated with PTX simultaneously into PLGA nanoparticles. After that, the non-complex was conjugated with Pep-1 through chemical modification. The resulting Pep-NP-SPION/PTX showed a spherical morphology and an average size of 100 nm. The enhancement cellular uptake of Pep-NP-SPION was demonstrated in in vitro through cell experiments. The IC50 value of Pep-NP-SPION/PTX and NP-SPION/PTX was determined to be 10.2 and 19.4 μg/mL, respectively. A biodistribution study showed that obvious higher accumulations of Pep-NP-SPION was observed in tumors, compared with that of non-targeting nanocomposites. Moreover, under the condition of a magnetic field, both NP-SPION and Pep-NP-SPION exhibited much higher tumor distribution. Furthermore, Pep-NP-SPION/PTX presented desirable in vivo anti-tumor effects based on active targeting and magnetic targeting characteristics. Altogether, Pep-NP-SPION/PTX can offer magnetic targeting and receptor mediated targeting to enhance the anti-tumor outcome

An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway.

In invertebrates, small interfering RNAs are at the vanguard of cell-autonomous antiviral immunity. In contrast, antiviral mechanisms initiated by interferon (IFN) signaling predominate in mammals. Whilst mammalian IFN-induced miRNA are known to inhibit specific viruses, it is not known whether host-directed microRNAs, downstream of IFN-signaling, have a role in mediating broad antiviral resistance. By performing an integrative, systematic, global analysis of RNA turnover utilizing 4-thiouridine labeling of newly transcribed RNA and pri/pre-miRNA in IFN-activated macrophages, we identify a new post-transcriptional viral defense mechanism mediated by miR-342-5p. On the basis of ChIP and site-directed promoter mutagenesis experiments, we find the synthesis of miR-342-5p is coupled to the antiviral IFN response via the IFN-induced transcription factor, IRF1. Strikingly, we find miR-342-5p targets mevalonate-sterol biosynthesis using a multihit mechanism suppressing the pathway at different functional levels: transcriptionally via SREBF2, post-transcriptionally via miR-33, and enzymatically via IDI1 and SC4MOL. Mass spectrometry-based lipidomics and enzymatic assays demonstrate the targeting mechanisms reduce intermediate sterol pathway metabolites and total cholesterol in macrophages. These results reveal a previously unrecognized mechanism by which IFN regulates the sterol pathway. The sterol pathway is known to be an integral part of the macrophage IFN antiviral response, and we show that miR-342-5p exerts broad antiviral effects against multiple, unrelated pathogenic viruses such Cytomegalovirus and Influenza A (H1N1). Metabolic rescue experiments confirm the specificity of these effects and demonstrate that unrelated viruses have differential mevalonate and sterol pathway requirements for their replication. This study, therefore, advances the general concept of broad antiviral defense through multihit targeting of a single host pathway

Study of the interferon-oxysterol antiviral response and 3-Hydroxy-3-Methylglutaryl-CoA Reductase

The oxysterol, 25-hydroxycholesterol (25-HC), is important for sterol metabolism and emerging evidence suggests that 25-HC plays a more critical role in immunity and infection. However, the precise antiviral mechanism and the target of 25- HC remains unclear. Here efforts were made to investigate the link between viral infection and the triggering of the 25-HC associated interferon (IFN) response, and how this dynamically alters the endogenous level of 3-hydroxy- 3-methylglutaryl-CoA reductase (HMGCR), a key enzyme that catalyses the production of the precursor of cholesterol and oxysterols. In this thesis I have sought to specifically explore the temporal changes and role of HMGCR in DNA virus (cytomegalovirus) and RNA (Influenza) virus infections. I hypothesise that HMGCR is a target for 25-HC associated IFN-mediated host defence against viral infection. To characterise HMGCR and test this hypothesis, the following objectives were defined: (1). To establish an experimental system to quantitatively study the endogenous HMGCR protein level; (2). To investigate the mechanism of the down-regulation of HMGCR involved in the IFN-mediated innate immune response; (3). To study the behaviour of HMGCR in the influenza virus induced 25-HC associated IFN-mediated innate immune response; (4). To study the behaviour of HMGCR in the cytomegalovirus induced 25-HC associated IFN-mediated innate immune response. Chapter 3, describes establishing an experimental system for the quantification of endogenous HMGCR levels. Different protein detection methods, including a modified western blot protocol and immunostaining, were tested. The results of RNA interference of HMGCR demonstrate that under lipid-deficient condition with the supplementation of mevastatin (an HMGCR inhibitor) the modified western blot protocol specifically detects endogenous HMGCR. This chapter lays the foundational work for the temporal analysis and testing the role of HMGCR in infection. In Chapter 4, the mechanism of the degradation of HMGCR following 25-HC and IFN treatments, in wild-type and Ch25h−/− mouse bone marrow derived macrophages (BMDMs), was investigated. Similar to 25-HC, IFN-γ treatment results in the drop of both the transcript and protein abundance of HMGCR in wild-type BMDMs. Differential temporal analysis of RNA and protein alterations and the use of proteasome inhibitors reveals that both 25-HC and IFN-γ lead to a marked reduction of HMGCR protein via a proteasomal degradation mechanism within early times of treatments. Further, the immediate reduction of HMGCR levels induced by IFN-γ was completely abrogated in Ch25h−/− BMDMs. Hence, the reduction of HMGCR following IFN-γ treatment is due to the de novo synthesis in macrophages of 25-HC. However, the decrease of Hmgcr gene expression was observed in not only wild-type but also Ch25h−/− BMDMs, suggesting additional mechanisms for regulating Hmgcr RNA levels. These results demonstrate the mechanism of the down-regulation of HMGCR resulted from the induction of IFN response during viral infection, is only partially due the de novo synthesis of 25-HC. In chapter 5, influenza A virus was used to investigate the role of HMGCR in the IFN-mediated innate immune response. The inhibition of HMGCR by RNA interference inhibited viral growth, suggesting the requirement of HMGCR for optimal intracellular viral growth. Viral infection in wild-type murine BMDMs reduced the endogenous HMGCR levels. However, the reduction of HMGCR at early times was prevented in Ch25h−/− BMDMs. Intriguingly, the decrease of HMGCR at late time points was still observed in Ch25h−/− BMDMs. These results indicate that the down-regulation of HMGCR with influenza virus infection in BMDMs at early times is completely due to the de novo synthesis of 25-HC; whereas at late times alternative pathways or mechanisms exist. Additionally, human epithelial A549 cells and A549/PIV5-V cells that are deficient in STAT1 were used to study the role of IFN pathway in the down-regulation of HMGCR at late times during viral infection. Results from these studies show that at late times the reduction of HMGCR is due to IFN-independent mechanisms. Chapter 6, extends these investigations to the herpes virus murine cytomegalovirus and infection of BMDMs. HMGCR is known to be essential for cytomegaloviral infections and 25-HC, statin and RNAi inhibition of HMGCR restrict viral growth. 25-HC is shown to reduce HMGCR at immediate early times of infection. However, most notably, the down-regulation of HMGCR was also observed in Ch25h−/− BMDMs at late times with murine cytomegalovirus infected BMDMs. These results confirm that alternative pathways or mechanisms exist, playing roles in the crosstalk between cholesterol metabolism and innate immune response. Collectively, this study characterises the role of HMGCR in the 25-HC associated IFN-mediated host defence against viral infection. Results indicate that, in addition to the IFN-mediated host response, alternative pathways or other mechanisms also result in the down-regulation of HMGCR during viral infection. HMGCR is at the crossroad of different pathways or mechanisms, and is therefore not only targeted by 25-HC. Hence, further questions can be addressed from these results: (1). What are the alternative pathways or mechanisms for the down-regulation of HMGCR? (2). How do these pathways or mechanisms work in hosts’ immune system? Answering these questions can contribute to refining the pathway map of innate immunity and understanding the precise role of HMGCR, or even the sterol biosynthesis pathway, in hosts’ immune response against pathogens

Structured model selection via ℓ1−ℓ2\ell_1-\ell_2 optimization

Automated model selection is an important application in science and engineering. In this work, we develop a learning approach for identifying structured dynamical systems from undersampled and noisy spatiotemporal data. The learning is performed by a sparse least-squares fitting over a large set of candidate functions via a nonconvex $\ell_1-\ell_2$ sparse optimization solved by the alternating direction method of multipliers. Using a Bernstein-like inequality with a coherence condition, we show that if the set of candidate functions forms a structured random sampling matrix of a bounded orthogonal system, the recovery is stable and the error is bounded. The learning approach is validated on synthetic data generated by the viscous Burgers' equation and two reaction-diffusion equations. The computational results demonstrate the theoretical guarantees of success and the efficiency with respect to the ambient dimension and the number of candidate functions.Comment: Wanted to revis

Dynamic constitutive behavior investigation of a novel low alloy ultra-high strength steel

The goal of this work is to reveal the dynamic mechanical properties and constitutive relationship of a novel low alloy ultra-high strength DT506 steel under high strain rates. The quasi-static state and dynamic compression behavior of the material at the strain rates of 10 ^−3 –10 ^3 s ^−1 were examined using an MTS landmark electro-hydraulic servo universal tester and a Split-Hopkinson bar (SHPB). The results show that DT506 steel is a strain-rate-sensitive material that shows an increase in strength with increasing strain rate. Based on the quasi-static and dynamic compression data, the parameters in the Cowper-Symonds (C-S) and the Johnson-Cook (J-C) models are determined. Since the previously developed models are cannot accurately predict the effect of the strain rate. A new theoretical model is obtained through the optimization of the parameters in the standard J-C model. The optimized model greatly improves the prediction accuracy of the true stress-strain dynamic behavior of materials. This new model is helpful for the verification of the underlying mechanism of the dynamic behavior of the material. Test results may provide basic data for future research on dynamic mechanical properties and constitutive relationship of metal alloys

Mass transfer between sandstones and interbedded mudstones: Impact on petroleum charge, Bohai Bay Basin, China

The Permo-Carboniferous sandstones in the Gubei area, Bohai Bay Basin, are reservoirs for large accumulations of natural gas. The natural gas accumulations only occur in the sandstone beds thicker than 1.9 m. Moreover, the maximum porosity of every bed correlates positively with bed thickness up to 2.0 m and for thicker beds porosity is uniform. Porosity transitional zones developed at the top and bottom of each bed, with mean thicknesses of 1.25 m and 0.75 m, respectively. Porosity shows a positive correlation with the distance to the sandstone/mudstone contact in the zones. Interpretations based upon an extensive petrographic and geochemical database indicate that the sandstones experienced a mass fluid input from the adjacent mudstones during the early diagenesis. The infiltration resulted in extensive clay coats and pore-filling cements in sandstones, which were effective for inhibiting dissolution of grains during subsequent diagenesis process. The mass introduction only affected the marginal parts of the sandstones within 1.25 m of the top and 0.75 m of the bottom of every bed, causing thin sandstone beds with thickness of approximately 2 m to be tightly cemented totally. Thus the central parts of each (thicker) beds became preferential sites for the natural gas accumulation. The differential levels of cementation in thin and thick sandstone beds observed here has significant implications for exploration of similar interbedded sandstone and shale sequences elsewhere including shale gas targets

The Vitamin D3 Synthesis Pathway

<p>A pathway diagram describing the synthesis of vitamin D3 and its relationship to the cholesterol synthesis pathway, obtained from a review of the published literature as part of the project work for our MSc in Genomics and Pathway Biology. The pathway is presented in SBGN notation. This pathway diagram has not been peer reviewed.</p

Integrative analysis identifies cancer cell-intrinsic RARRES1 as a predictor of prognosis and immune response in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a subtype of breast cancer with poor prognosis and limited treatment options. Although immune checkpoint inhibitors (ICIs) have been proven to improve outcomes in TNBC patients, the potential mechanisms and markers that determine the therapeutic response to ICIs remains uncertain. Revealing the relationship and interaction between cancer cells and tumor microenvironment (TME) could be helpful in predicting treatment efficacy and developing novel therapeutic agents. By analyzing single-cell RNA sequencing dataset, we comprehensively profiled cell types and subpopulations as well as identified their signatures in the TME of TNBC. We also proposed a method for quantitatively assessment of the TME immune profile and provided a framework for identifying cancer cell-intrinsic features associated with TME through integrated analysis. Using integrative analyses, RARRES1 was identified as a TME-associated gene, whose expression was positively correlated with prognosis and response to ICIs in TNBC. In conclusion, this study characterized the heterogeneity of cellular components in TME of TNBC patients, and brought new insights into the relationship between cancer cells and TME. In addition, RARRES1 was identified as a potential predictor of prognosis and response to ICIs in TNBC