Complementary Omics Strategies to Dissect p53 Signaling Networks Under Nutrient Stress

Signaling trough p53 is a major cellular stress response mechanism and increases upon nutrient stresses such as starvation. Here, we show in a human hepatoma cell line that starvation leads to robust nuclear p53 stabilization. Using BioID, we determine the cytoplasmic p53 interaction network within the immediate-early starvation response and show that p53 is dissociated from several metabolic enzymes and the kinase PAK2 for which direct binding with the p53 DNA-binding domain was confirmed with NMR studies. Furthermore, proteomics after p53 immunoprecipitation (RIME) uncovered the nuclear interactome under prolonged starvation, where we confirmed the novel p53 interactors SORBS1 (insulin receptor signaling) and UGP2 (glycogen synthesis). Finally, transcriptomics after p53 re-expression revealed a distinct starvation-specific transcriptome response and suggested previously unknown nutrient-dependent p53 target genes. Together, our complementary approaches delineate several nodes of the p53 signaling cascade upon starvation, shedding new light on the mechanisms of p53 as nutrient stress sensor. Given the central role of p53 in cancer biology and the beneficial effects of fasting in cancer treatment, the identified interaction partners and networks could pinpoint novel pharmacologic targets to fine-tune p53 activity.

SWCNH (Single walled carbon nanohorn) supervises ER (Endoplasmic reticulum) stress through triggering autophagy process of hepatocytes, especially in hepatoma cell line HepG2

Backgrounds: The cellular homeostasis is major maintained by the catabolic pathway of autophagy. Our previous work indicated that SWCNH were associated with endoplasmic reticulum (ER) stress mediated by calcium flow and autophagic response. But, its mechanism was unclear. Methods: The regulation of SWCNH on the calcium flow then autophagy of liver cells were investigated through inducing ER stress with tunicamycin and SWCNH. The calcuim flow was determined using Fluo-3, then autophagy was examined with immunofluorescence or western blot for LC3, Beclin-1, ATG-5, and p62. Moreover, the apopototic protein of Bax and Bcl-2 was detected, too. Results: Tunicamycin-induced ER stress in hepatocytes was related to calcium flow, especially for hepatoma cell line HepG2. Moreover, SWCNH participated in the regulation of endoplasmic reticulum stress-related calcium flow. Besides, SWCNH induced hepatocyte autophagy and inhibited cell apoptosis, then mediated the process of hepatocyte autophagy. Conclusions: Tunicamycin-induced ER stress in hepatocytes was related to calcium flow. Moreover, SWCNH induced hepatocyte autophagy, inhibited cell apoptosis, and participated in the autophagy regulation of hepatocyte, especially for hepatoma cell line.

Isolation and Characterization of SARS-CoV-2 strains circulating in Eastern India.

Emergence of SARS-CoV-2 as a serious pandemic has altered the global socioeconomic dynamics. The wide prevalence, high death counts and rapid emergence of new variants urge for establishment of research infrastructure to facilitate rapid development of efficient therapeutic modalities and preventive measures. In agreement with this, five SARS-CoV2 strains (ILS01, ILS02, ILS03, ILS15 and ILS24) of four different clades (19A, 19B, 20A and 20B) were isolated from patient swab samples collected during the 1st COVID-19 wave in Odisha, India. The viral isolates were adapted to in-vitro cultures and further characterized to identify strain specific variations in viral growth characteristics. All the five isolates showed substantial amount of virus induced CPE however ILS03 belonging to 20A clade displayed highest level of CPE. Time kinetics experiment revealed spike protein expression was evident after 16th hours post infection in all five isolates. ILS03 induced around 90% of cytotoxicity. Further, the susceptibility of various cell lines (human hepatoma cell line (Huh-7), CaCo2 cell line, HEK-293T cells, Vero, Vero-E6, BHK-21, THP-1 cell line and RAW 264.7 cells) were assessed. Surprisingly, it was found that the human monocyte cells THP-1 and murine macrophage cell line RAW 264.7 were permissive to all the SARS-CoV-2 isolates. The neutralization susceptibility of viral isolates to vaccine-induced antibodies was determined using sera from individuals vaccinated in the Government run vaccine drive in India. The micro-neutralization assay suggested that both Covaxin and Covishield vaccines were equally effective (100% neutralization) against all of the isolates. The whole genome sequencing of culture adapted viral isolates and viral genome from patient oropharyngeal swab sample suggested that repetitive passaging of SARS-CoV2 virus in Vero-E6 cells did not lead to emergence of many mutations during the adaptation in cell culture. Phylogenetic analyses revealed that the five isolates clustered to respective clades. The major goal was to isolate and adapt SARS-CoV-2 viruses in in-vitro cell culture with minimal modification to facilitate research activities involved in understanding the molecular virology, host-virus interactions, application of these strains for drug discovery and animal challenge models development which eventually will contribute towards the development of effective and reliable therapeutics.

Experimental Study of Rhein Inhibits the Invasion and Migration of HepG2 Cells by ERK Signaling Pathway

Objective: To investigate the effectiveness of Rhein on the proliferation, invasion and migration of human hepatoma cell line HepG2 and its possible mechanism.Methods: Human hepatoma cell line HepG2 was treated with different concentrations of Rhein (Rhein treatment group) and culture in culture medium alone (control group).The proliferation activity of the cells was determined by methyl Thiazolyl Tetrazolium (MTT) colorimetry.Transwell assay detected the invasion and migration of cells in each group.Cell scratch test was used to detect the migration ability of cells in each group.Excella-phospho-excellar signal-regulated kinase (P-ERK) activity was determined by ELISA after treatment with 50μ mol/L Rhein at different times.Western blot was used to detect ERK protein expression in HepG2 cells treated with 50 μmol/L Rhein.Results: Compared with the control group, the proliferation activity, invasion and migration ability of HepG2 cells in the Rhein treatment group were all decreased (P< 0.05), and the p-ERK relative activity of HepG2 cells treated with Rhein was decreased (P < 0.05).Conclusion: Rhein inhibits the invasion and migration of HCC cells, possibly by inhibiting the ERK pathway

Dissecting the Mechanisms of Hepcidin and BMP-SMAD Pathway Regulation By FKBP12

The BMP-SMAD pathway is activated when a dimeric ligand (BMP) interacts with a dimeric serine threonine kinase receptor (BMPRII) and triggers the activation of a dimeric BMP type I receptor (BMPRI). Catalytically active BMPRIs phosphorylate SMAD1/5/8 that, upon SMAD4 binding, translocate to the nucleus to regulate the expression of BMP target genes, including hepcidin. Hepcidin is the main regulator of iron homeostasis that controls body iron levels by binding and blocking the sole iron exporter ferroportin. In agreement, hepcidin expression is homeostatically activated by serum and liver iron, and its deficiency is a common hallmark of Hereditary Hemochromatosis (HH) and the major cause of iron overload in beta thalassemia. The components of the BMP-SMAD pathway relevant for hepcidin regulation are ALK2 and ALK3 (BMPRI); BMPR2 and ACVR2A (BMPRII), BMP2 and BMP6 (BMP ligands). Recently, we have identified the immunophilin FKBP12 as an inhibitor of hepcidin and demonstrated that FKBP12 binds ALK2 to avoid ligand-independent activation of the BMP-SMAD pathway. To investigate the mechanism of BMP-SMAD pathway and hepcidin regulation by FKBP12, we performed in vitro, ex vivo and in vivo studies. We found that FKBP12 sequestration by the immunosuppressive drug Tacrolimus (TAC) stabilizes ALK2-ALK2 homodimers and ALK2-ALK3 heterodimers in a transfected human hepatoma cell line. In addition, it increases the interaction of ALK2 with ACVR2A and BMPR2. To investigate the role of FKBP12 on BMP-SMAD signaling, BMPRI and II were silenced in murine primary hepatocytes. Despite FKBP12 co-immunoprecipitates only with ALK2, silencing of Alk2 and Alk3 completely blunts TAC-mediated BMP-SMAD pathway activation, suggesting that FKBP12 functionally interacts also with ALK3. Acvr2a silencing impairs TAC-dependent hepcidin upregulation, whereas Bmpr2 silencing does not. As expected, Fkbp12 silencing abrogates hepcidin upregulation by TAC, confirming the main role of this immunophilin in hepcidin regulation. In vivo, TAC treatment upregulates hepcidin in wild type and HH mouse models, but surprisingly, Fkbp12 mRNA downregulation by ASOs does not. Interestingly, Fkbp 2, 4 and 8 are highly expressed in murine hepatocytes and, according to literature data, are able to bind to TAC. Of note, Fkbp12 is the least expressed immunophilin in murine primary hepatocytes. To further investigate the FKBPs involved in TAC-dependent hepcidin regulation, Fkbp2, 4 and 8 were knockdown in murine primary HCs that were then treated with TAC. The TAC effect is preserved in siFkbp2- and siFkbp4-derived HCs, but abolished when Fkbp8 was downregulated. Overall these data suggest that: 1) FKBP12 regulates BMP-SMAD signaling by favoring ALK2-ALK3 homo and heterodimerization, and interaction with BMPRII in the absence of ligands; 2) TAC-mediated hepcidin upregulation is dependent upon ALK2, ALK3, ACVR2A, FKBP12 and FKBP8. 3) In vivo, TAC treatment upregulates hepcidin whereas Fkbp12 silencing does not, suggesting the existence of redundancy between the different FKBPs. Further studies are needed to dissect the role of FKBP8 in BMP-SMAD pathway and hepcidin regulation. Disclosures Aghajan: Ionis Pharmaceuticals, Inc.: Current Employment. Muckenthaler: Silence Therapeutics: Research Funding. Guo: Ionis Pharmaceuticals, Inc.: Current Employment.

Layered Double Hydroxides as A Drug Delivery Vehicle for S-Allyl-Mercapto-Cysteine (SAMC)

The intercalations of anionic molecules and drugs in layered double hydroxides (LDHs) have been intensively investigated in recent years. Due to their properties, such as versatility in chemical composition, good biocompatibility, high density and protection of loaded drugs, LDHs seem very promising nanosized systems for drug delivery. In this work, we report the intercalation of S-allyl-mercapto-cysteine (SAMC), which is a component of garlic that is well-known for its anti-tumor properties, inside ZnAl-LDH (hereafter LDH) nanostructured crystals. In order to investigate the efficacy of the intercalation and drug delivery of SAMC, the intercalated compounds were characterized using X-ray powder diffraction (XRD), Fourier-transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). The increase in the interlayer distance of LDH from 8.9 Å, typical of the nitrate phase, to 13.9 Å indicated the intercalation of SAMC, which was also confirmed using FT-IR spectra. Indeed, compared to that of the pristine LDH precursor, the spectrum of LDH-SAMC was richly structured in the fingerprint region below 1300 cm−1, whose peaks corresponded to those of the functional groups in the SAMC molecular anion. The LDH-SAMC empirical formula, obtained from UV-Vis spectrophotometry and thermogravimetric analysis, was [Zn0.67Al0.33(OH)2]SAMC0.15(NO3)0.18·0.6H2O. The morphology of the sample was investigated using SEM: LDH-SAMC exhibited a more irregular size and shape of the flake-like crystals in comparison with the pristine LDH, with a reduction in the average crystallite size from 3 µm to about 2 µm. In vitro drug release studies were performed in a phosphate buffer solution at pH 7.2 and 37 °C and were analyzed using UV-Vis spectrophotometry. The SAMC release from LDH-SAMC was initially characterized by a burst effect in the first four hours, during which, 32% of the SAMC is released. Subsequently, the release percentage increased at a slower rate until 42% after 48 h; then it stabilized at 43% and remained constant for the remaining period of the investigation. The LDH-SAMC complex that was developed in this study showed the improved efficacy of the action of SAMC in reducing the invasive capacity of a human hepatoma cell line.

Development of a Hybrid Polymer-Based Microfluidic Platform for Culturing Hepatocytes towards Liver-on-a-Chip Applications

The drug development process can greatly benefit from liver-on-a-chip platforms aiming to recapitulate the physiology, mechanisms, and functionalities of liver cells in an in vitro environment. The liver is the most important organ in drug metabolism investigation. Here, we report the development of a hybrid cyclic olefin copolymer (COC) and polydimethylsiloxane (PDMS) microfluidic (HCP) platform to culture a Huh7 hepatoma cell line in dynamic conditions towards the development of a liver-on-a-chip system. The microfluidic platform is comprised of a COC bottom layer with a microchannel and PDMS-based flat top layer sandwiched together. The HCP device was applied for culturing Huh7 cells grown on a collagen-coated microchannel. A computational fluid dynamics modeling study was conducted for the HCP device design revealing the presence of air volume fraction in the chamber and methods for optimizing experimental handling of the device. The functionality and metabolic activity of perfusion culture were assessed by the secretion rates of albumin, urea, and cell viability visualization. The HCP device hepatic culture remained functional and intact for 24 h, as assessed by resulting levels of biomarkers similar to published studies on other in vitro and 2D cell models. The present results provide a proof-of-concept demonstration of the hybrid COC–PDMS microfluidic chip for successfully culturing a Huh7 hepatoma cell line, thus paving the path towards developing a liver-on-a-chip platform.

Structure, Antioxidant Activity and In Vitro Hypoglycemic Activity of a Polysaccharide Purified from Tricholoma matsutake

The structure, antioxidant activity and hypoglycemic activity in vitro of a novel homogeneous polysaccharide from Tricholoma matsutake (Tmp) were investigated. Structural features suggested that Tmp was consisted of arabinose (Ara), mannose (Man), glucose (Glc) and galactose (Gal) with a molar ratio of 1.9:13.6:42.7:28.3, respectively, with a molecular weight of 72.14 kDa. The structural chain of Tmp was confirmed to contain →2,5)-α-l-Arabinofuranose (Araf)-(1→, →3,5)-α-l-Araf-(1→, β-d-Glucopyranose (Glcp)-(1→, α-d-Mannopyranose (Manp)-(1→, α-d-Galacopyranose (Galp)-(1→, →4)-β-d-Galp-(1→, →3)-β-d-Glcp-(1→, →3)-α-d-Manp-(1→, →6)-3-O-Methyl (Me)-α-d-Manp-(1→, →6)-α-d-Galp-(1→, →3,6)-β-d-Glcp-(1→, →6)-α-d-Manp-(1→ residues. Furthermore, Tmp possessed strong antioxidant activity and showed the strong inhibitory effect on α-glucosidase and α-amylase activities. Then, a further evaluation found that there was a dramatic improvement in the glucose consumption, glycogen synthesis and the activities of pyruvate kinase and hexokinase when the insulin-resistant-human hepatoma cell line (IR-HepG2) was treated with Tmp. The above results indicated that Tmp had good hypoglycemic activity and also exhibited great potentials in in terms of dealing with type 2 diabetes mellitus.

Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology

Interferons (IFNs) are key cytokines involved in alerting the immune system to viral infection. After IFN stimulation, cellular transcriptional profile critically changes, leading to the expression of several IFN stimulated genes (ISGs) that exert a wide variety of antiviral activities. Despite many ISGs have been already identified, a comprehensive network of coding and non-coding genes with a central role in IFN-response still needs to be elucidated. We performed a global RNA-Seq transcriptome profile of the HCV permissive human hepatoma cell line Huh7.5 and its parental cell line Huh7, upon IFN treatment, to define a network of genes whose coordinated modulation plays a central role in IFN-response. Our study adds molecular actors, coding and non-coding genes, to the complex molecular network underlying IFN-response and shows how systems biology approaches, such as correlation networks, network’s topology and gene ontology analyses can be leveraged to this aim.

Water-Active Titanium/Molybdenum/Mixed-Oxides: Removal Efficiency of Organic Water Pollutants by Adsorption and Photocatalysis and Toxicity Assessment

A new titanium/molybdenum/mixed-oxides (TMO) contact-type heterojunction photocatalyst was prepared by a simple, low-cost, and environmentally-friendly mixing-calcination solid-state method. A microstructural investigation by scanning electron microscopy (SEM) showsirregularly shaped agglomerated morphology of TMO that consists of firmly connected globular TiO2 and rod-like MoO3 particles. The detailed structure and optical bandgap investigation by X-ray diffraction, Raman, and UV-Vis spectroscopy revealed the TMO’s composition of ~37 wt.% rutile TiO2, ~25 wt.% of anatase TiO2, and ~38 wt.% of molybdite MoO3 phase and an absorption threshold of around 380 nm, which implies more probability of desirable higher visible light absorption. The removal efficiency of pesticides quinmerac (QUI) and tembotrione (TEM), and pharmaceuticals metoprolol (MET), amitriptyline (AMI), ciprofloxacin (CIP),and ceftriaxone (CEF) from water in the presence of starting pure TiO2, MoO3, and prepared TMO were investigated under different pH values and UV irradiation/simulated sunlight (SS). Each starting metal-oxide precursors and prepared TMO showed a different affinity for adsorption of tested pesticides and pharmaceuticals, and, in general, better photocatalytic degradation efficiency under UV irradiation than under simulated sunlight. The highest photocatalytic degradation efficiency under UV irradiation was 81.6% for TEM using TMO; using TiO2 was 65.0% for AMI, and using MoO3 was 79.3% for CEF after 135 min. However, TMO showed a very high synergic adsorption/photocatalytic under-SS efficiency in the removal of CIP of almost 80% and under UV irradiation of 90% CIP removal after 75 min. The toxicity of catalysts, starting compounds, and their intermediates formed during the removal process was assessed using a rat hepatoma cell line (H-4-II-E). The highest hepatotoxic effects were obtained by using UV irradiated QUI and MET suspension with TMO for up to 60 min.