Immune landscape of advanced gastric cancer tumor microenvironment identifies immunotherapeutic relevant gene signature

Background Advanced gastric cancer (AGC) is a disease with poor prognosis due to the current lack of effective therapeutic strategies. Immune checkpoint blockade treatments have shown effective responses in patient subgroups but biomarkers remain challenging. Traditional classification of gastric cancer (GC) is based on genomic profiling and molecular features. Therefore, it is critical to identify the immune-related subtypes and predictive markers by immuno-genomic profiling. Methods Single-sample gene-set enrichment analysis (ssGSEA) and ESTIMATE algorithm were used to identify the immue-related subtypes of AGC in two independent GEO datasets. Weighted gene co-expression network analysis (WGCNA) and Molecular Complex Detection (MCODE) algorithm were applied to identify hub-network of immune-related subtypes. Hub genes were confirmed by prognostic data of KMplotter and GEO datasets. The value of hub-gene in predicting immunotherapeutic response was analyzed by IMvigor210 datasets. MTT assay, Transwell migration assay and Western blotting were performed to confirm the cellular function of hub gene in vitro. Results Three immune-related subtypes (Immunity_H, Immunity_M and Immunity_L) of AGC were identified in two independent GEO datasets. Compared to Immunity_L, the Immuntiy_H subtype showed higher immune cell infiltration and immune activities with favorable prognosis. A weighted gene co-expression network was constructed based on GSE62254 dataset and identified one gene module which was significantly correlated with the Immunity_H subtype. A Hub-network which represented high immune activities was extracted based on topological features and Molecular Complex Detection (MCODE) algorithm. Furthermore, ADAM like decysin 1 (ADAMDEC1) was identified as a seed gene among hub-network genes which is highly associated with favorable prognosis in both GSE62254 and external validation datasets. In addition, high expression of ADAMDEC1 correlated with immunotherapeutic response in IMvigor210 datasets. In vitro, ADAMDEC1 was confirmed as a potential protein in regulating proliferation and migration of gastric cancer cell. Deficiency of ADAMDEC1 of gastric cancer cell also associated with high expression of PD-L1 and Jurkat T cell apoptosis. Conclusions We identified immune-related subtypes and key tumor microenvironment marker in AGC which might facilitate the development of novel immune therapeutic targets.

Deinking of Mixed Office Waste (MOW) Paper Using Enzymes

Deinking of Mixed Office Waste [MOW] paper was carried out by using a flotation device and adding enzymes as defibrillators. Employing the computational simulation of the molecular coupling between the cellulase enzyme obtained from Trichoderma sp. and cellulose, the enzyme-cellulose molecular complex and the main amino acids endo-β-1,4-D-glucanase of this molecule, responsible for the hydrolysis of cellulose, were obtained. Three of these amino acids were used for deinking. The deinked cellulose fibers were evaluated according to the standards of the paper industry (ISO whiteness [brightness], factor of reflectance, opacity, and tonality) to determine the efficiency of deinking. The experimental results show that the best optical characteristics of the sheets of deinked paper with amino acids are those where a mixture of aspartate, glutamate, and asparagine was applied, instead of their individual dosage. In addition to the aforesaid, the use of enzymes instead of the traditionally used reagent, such as sodium hydroxide, avoids the contamination of wastewater; additionally, the operation of the column is carried out easily, taking into consideration that the pH of the system goes from alkaline to neutral.

Complexation of Cyclodextrins with Benzoic Acid in Water-Organic Solvents: A Solvation-Thermodynamic Approach

The aim of this research is to obtain new data about the complexation between β-cyclodextrin (β-CD) and benzoic acid (BA) as a model reaction of the complex formation of hydrophobic molecules with cyclodextrins (CDs) in various media. This research may help developing cyclodextrin-based pharmaceutical formulations through the choice of the appropriate solvent mixture that may be employed in the industrial application aiming to control the reactions/processes in liquid phase. In this paper, NMR results for the molecular complex formation between BA and β-CD ([BA⊂β-CD]) in D2O-DMSO-d6 and in D2O-EtOH have shown that the stability of the complex in the H2O-DMSO-d6 varies within the experimental error, while decreases in H2O-EtOH. Changes in the Gibbs energy of BA resolvation in water and water–dimethylsulfoxide mixtures have been obtained and have been used in the analysis of the reagent solvation contributions into the Gibbs energy changes of the [BA⊂β-CD] molecular complex formation. Quantum chemical calculations of the interaction energy between β-CD and BA as well as the structure of the [BA⊂β-CD] complex and the energy of β-CD and BA interaction in vacuum and in the medium of water, methanol and dimethylsulfoxide solvents are carried out. The stability of [BA⊂β-CD] complex in H2O-EtOH and H2O-DMSO solvents, obtained by different methods, are compared. The thermodynamic parameters of the [BA⊂β-CD] molecular complexation as well as the reagent solvation contributions in H2O-EtOH and H2O-DMSO mixtures were analyzed by the solvation-thermodynamic approach.

The Mode of SN38 Derivatives Interacting with Nicked DNA Mimics Biological Targeting of Topo I Poisons

The compounds 7-ethyl-9-(N-methylamino)methyl-10-hydroxycamptothecin (2) and 7-ethyl-9-(N-morpholino)methyl-10-hydroxycamptothecin (3) are potential topoisomerase I poisons. Moreover, they were shown to have favorable anti-neoplastic effects on several tumor cell lines. Due to these properties, the compounds are being considered for advancement to the preclinical development stage. To gain better insights into the molecular mechanism with the biological target, here, we conducted an investigation into their interactions with model nicked DNA (1) using different techniques. In this work, we observed the complexity of the mechanism of action of the compounds 2 and 3, in addition to their decomposition products: compound 4 and SN38. Using DOSY experiments, evidence of the formation of strongly bonded molecular complexes of SN38 derivatives with DNA duplexes was provided. The molecular modeling based on cross-peaks from the NOESY spectrum also allowed us to assign the geometry of a molecular complex of DNA with compound 2. Confirmation of the alkylation reaction of both compounds was obtained using MALDI–MS. Additionally, in the case of 3, alkylation was confirmed in the recording of cross-peaks in the 1H/13C HSQC spectrum of 13C-enriched compound 3. In this work, we showed that the studied compounds—parent compounds 2 and 3, and their potential metabolite 4 and SN38—interact inside the nick of 1, either forming the molecular complex or alkylating the DNA nitrogen bases. In order to confirm the influence of the studied compounds on the topoisomerase I relaxation activity of supercoiled DNA, the test was performed based upon the measurement of the fluorescence of DNA stain which can differentiate between supercoiled and relaxed DNA. The presented results confirmed that studied SN38 derivatives effectively block DNA relaxation mediated by Topo I, which means that they stop the machinery of Topo I activity.

QUANTUM CHEMICAL SIMULATION OF THE INHIBITORY EFFECT OF AQUEOUS SOLUTIONS OF INORGANIC COPPER(II) SALTS ON THE COMBUSTION OF HYDROCARBONS

Introduction. The search for chemicals that would have an effective fire extinguishing effect and the development of new fire extinguishers based on them is an extremely important problem of fire safety. It is known from the literature that new aqueous fire extinguishing agents (AFEAs) based on dissolved inorganic salts of transition metals, in particular, copper(II) chloride salts, have a rather efficient inhibitory effect on the hydrocarbon flame. However, the mechanism of inhibition of hydrocarbon combustion by this class of substances is not completely ascertained. However, it is reliable information about the processes that take place in the flame after the bringing in there of the aerosol of the mentioned AFEA will allow a systematic search for more optimal chemical composition of dissolved inorganic salts of d-metals. Purpose. The purpose of the work is to reveal the peculiarities of the interaction of concentrated aqueous solutions of copper(II) chloride salts with chemically active flame particles.Methods. Quantum chemical calculations of the chemical activity of radicals that appear in the flame and the physicochemical processes that occur in the flame after the bringing on there of AFEA aerosol.Results. The mechanism of a fire-extinguishing effect of aqueous solutions of inorganic copper(II) salts on a hydrocarbon flame is investigated by a calculation method. The sequence of stages of chemical processes that occur in the flame during the inhibiting combustion of hydrocarbons by AFEAs—concentrated solutions of CuCl2 and K2[CuCl4]—and the thermal effects of all reactions that accompany each of these stepwise transformations were ascertained. The stages of the interaction of gaseous Cu2Cl4 molecules with ×OH and ×H radicals in flame with the formation of first a radical-molecular complex and then a molecular complex are decisive in the process of inhibition and display the processes of interruption of chain reactions, i.e. deactivation of radicals in a flame.Conclusion. Thus, using the method of quantum chemical calculations the mechanism of inhibition of hydrocarbon combustion by copper(II) salts was offered. The mechanism of this process is considered to be associative, the decisive elementary act of which is carried out according to the scheme of addition of active radicals of a flame (×OH particles) to gaseous molecules Cu2Cl4 with the formation of radical-molecular complex [{Cu(×OH)Cl2}2] and with its subsequent deactivation by ×H particles.

PreDarwinian evolution, prebiotic change: a principle of least selection

Evolution prior to its Darwinian era was an age of variation. Events allowed by starting materials, chemistry and physics were realized, directed by intrinsic probabilities. In this landscape, a principle of least selection defines the most probable evolutionary path. For selection from a population where x varies, the rate of x evolution dx/dt = αΔμ. μ is the population mean of the selected property x, [alpha] a proportionality constant. Explicit equations for selected change Δμ are presented. Simple results exist for frequent cases; for example, selection for x ≥ a threshold. Maximizing Δμ minimizes need for selection. Least selections for x demand maximal selection dependence on x, maximal x standard deviation σ, and maximal lower x threshold (consistent with the need for a survivor). Least selection is free of the cost of natural selection, thus can support rapid advance. Least selection also unites previous seemingly independent optima. As examples, evolution via ′starting bloc selection [prime] and ′chance utility′ (where selection spans a minimal change) and ′near-ideal reactions′ (where variable reactant supplies create easy reactions) occur via transitory paths of least selection. ′Bayesian convergence′ is guaranteed by least selection′s extremum (which sharply defines evolution′s path). [prime]Distribution fitness′ (where specific outcomes are selected among multiple concurrent variations) is least selection of rare functional minorities. Inheritance of encoded chemical capabilities first evolves because templating and catalysis are close, potentially joined in a single molecular complex. Least selection defines directions, biostructures define destinations in likely pathways of preDarwinian evolution.

Nuclear expression of VDR and AHR is mutually exclusive in glandular cells in endometriosis

The vitamin D receptor (VDR) and aryl hydrocarbon receptor (AHR) are two nuclear receptors that exert their effects by binding with ligands and forming a molecular complex. These complexes translocate to the nucleus and activate the expression of a series of genes which have a response element to VDR or AHR. Both receptors have been identified in the pathogenesis of endometriosis, a common disease characterized by the formation of endometrium-like tissue in ectopic zones. Despite numerous therapies, there is no definitive cure for endometriosis at the pharmacological level. Our study aims to describe the location and the expression of VDR and AHR at the protein level. For this purpose, an evaluation was performed using tissue from the three normal phases of the endometrium (proliferative, early, and late secretory) and in endometriosis by immunohistochemistry, using anti-VDR and anti-AHR antibodies. We demonstrate that in the nuclei of glandular cells in endometriosis, the expression of VDR and AHR is mutually exclusive—when the expression of one receptor is high, the other one is low—suggesting a possible target in the treatment of endometriosis. We also identify a significant change in the expression of glandular cytoplasmic AHR between the proliferative and late secretory endometrium.

The molecular complex of ciliary and golgin protein is critical for skull development

Intramembranous ossification, which consists of direct conversion of mesenchymal cells to osteoblasts, is a characteristic process in skull development. One critical role of these osteoblasts is to secrete collagen-containing bone matrix. However, it remains unclear how the dynamics of collagen trafficking is regulated during skull development. Here, we reveal the regulatory mechanisms of ciliary and golgin proteins required for intramembranous ossification. During normal skull formation, osteoblasts residing on the osteogenic front actively secreted collagen. Mass spectrometry and proteomic analysis determined endogenous binding between ciliary protein IFT20 and golgin protein GMAP210 in these osteoblasts. Like in Ift20 mutant mice, disruption of neural-crest specific GMAP210 in mice caused osteopenia-like phenotypes due to dysfunctional collagen trafficking. Mice lacking both IFT20 and GMAP210 displayed more severe skull defects compared to either IFT20 or GMAP210 mutants. These results demonstrate that the molecular complex of IFT20 and GMAP210 is essential for the intramembranous ossification during skull development.