Post-translational modifications of prostaglandin-endoperoxide synthase 2 in colorectal cancer: An update

Crosstalk between P2Y receptors and cyclooxygenase activity in inflammation and tissue repair

The role of extracellular nucleotides as modulators of inflammation and cell stress is well established. One of the main actions of these molecules is mediated by the activation of purinergic receptors (P2) of the plasma membrane. P2 receptors can be classified according to two different structural families: P2X ionotropic ion channel receptors, and P2Y metabotropic G protein-coupled receptors. During inflammation, damaged cells release nucleotides and purinergic signaling occurs along the temporal pattern of the synthesis of pro-inflammatory and pro-resolving mediators by myeloid and lymphoid cells. In macrophages under pro-inflammatory conditions, the expression and activity of cyclooxygenase 2 significantly increases and enhances the circulating levels of prostaglandin E2 (PGE2), which exerts its effects both through specific plasma membrane receptors (EP1-EP4) and by activation of intracellular targets. Here we review the mechanisms involved in the crosstalk between PGE2 and P2Y receptors on macrophages, which is dependent on several isoforms of protein kinase C and protein kinase D1. Due to this crosstalk, a P2Y-dependent increase in calcium is blunted by PGE2 whereas, under these conditions, macrophages exhibit reduced migratory capacity along with enhanced phagocytosis, which contributes to the modulation of the inflammatory response and tissue repair.

Elucidating the molecular mechanisms underlying anti-inflammatory effects of Morchella esculenta in the arachidonic acid metabolic pathway by network pharmacology and molecular docking

Morchella esculenta is an edible fungus with a uniquely delicious flavor and remarkable benefits for health. Herein, the molecular mechanism underlying the anti-inflammatory effects of Morchella esculenta was elucidated using molecular docking and network pharmacology. NPASS, Super-pred, SEA, Swiss Target Prediction, GeneCards, DisGeNET, Omim database, and STRING platform were used to select anti-inflammatory targets and construct target protein interaction networks using the active ingredients of Morchella esculenta. The OmicShare cloud platform was used to analyze GO functions and KEGG pathways related to the target, and the AutoDock Vina software was used to perform molecular docking and molecular dynamics (MD) simulation on the main target. Based on Cytoscape's "Network Analysis", the degree was used to identify potential key targets, and different inflammatory transcriptome data sets were used to evaluate core targets showing clinical significance. The active ingredient of Morchella esculenta identified from the NPASS database was EOYA, which had 43 anti-inflammatory targets, including NR1I2, PTGS1, PTGS2, CYP4F2, CYP3A4, TLR4, MAPK1, PLA2G4A, and PTPN11, and was mainly implicated in arachidonic acid metabolism, vascular endothelial growth factor signal pathway, and sphingomyelin signal transduction pathway, indicating that the anti-inflammatory effects of EOYA were mainly related to these biological processes. The degree was used to select 9 potential effective targets, namely NR1I2, PTGS1, PTGS2, CYP4F2, CYP3A4, TLR4, MAPK1, PLA2G4A, and PTPN11, among which NR1I2, PTGS1, PTGS2, PLA2G4A, MAPK1, CYP3A4, and TLR4 showed clinical significance. Molecular docking results showed that (E)-Octadec-11-En-9-Ynoic Acid (EOYA) could spontaneously bind to the 9 core targets, and the binding fractions of NR1I2, PTGS1, PTGS2, CYP4F2, and CYP3A4 were the highest. The MD simulation results showed that EYOA did indeed bind well NR1I2 to PTGS2, and the complex has high stability. Morchella esculenta can regulate the activity of prostaglandin endoperoxide synthetase, and affect the biosynthesis of prostaglandins, thereby impacting the metabolic pathway of arachidonic acid.

DEDTI versus IEDTI: efficient and predictive models of drug-target interactions

Drug repurposing is an active area of research that aims to decrease the cost and time of drug development. Most of those efforts are primarily concerned with the prediction of drug-target interactions. Many evaluation models, from matrix factorization to more cutting-edge deep neural networks, have come to the scene to identify such relations. Some predictive models are devoted to the prediction's quality, and others are devoted to the efficiency of the predictive models, e.g., embedding generation. In this work, we propose new representations of drugs and targets useful for more prediction and analysis. Using these representations, we propose two inductive, deep network models of IEDTI and DEDTI for drug-target interaction prediction. Both of them use the accumulation of new representations. The IEDTI takes advantage of triplet and maps the input accumulated similarity features into meaningful embedding corresponding vectors. Then, it applies a deep predictive model to each drug-target pair to evaluate their interaction. The DEDTI directly uses the accumulated similarity feature vectors of drugs and targets and applies a predictive model on each pair to identify their interactions. We have done a comprehensive simulation on the DTINet dataset as well as gold standard datasets, and the results show that DEDTI outperforms IEDTI and the state-of-the-art models. In addition, we conduct a docking study on new predicted interactions between two drug-target pairs, and the results confirm acceptable drug-target binding affinity between both predicted pairs.

Emerging Role of Plant-Based Dietary Components in Post-Translational Modifications Associated with Colorectal Cancer

Colorectal cancer (CRC) is one of the most common cancers worldwide. Its main modifiable risk factors are diet, alcohol consumption, and smoking. Thus, the right approach through lifestyle changes may lead to its prevention. In fact, some natural dietary components have exhibited chemopreventive activity through modulation of cellular processes involved in CRC development. Although cancer is a multi-factorial process, the study of post-translational modifications (PTMs) of proteins associated with CRC has recently gained interest, as inappropriate modification is closely related to the activation of cell signalling pathways involved in carcinogenesis. Therefore, this review aimed to collect the main PTMs associated with CRC, analyse the relationship between different proteins that are susceptible to inappropriate PTMs, and review the available scientific literature on the role of plant-based dietary compounds in modulating CRC-associated PTMs. In summary, this review suggested that some plant-based dietary components such as phenols, flavonoids, lignans, terpenoids, and alkaloids may be able to correct the inappropriate PTMs associated with CRC and promote apoptosis in tumour cells.

Identification of differentially expressed genes and pathways in diquat and paraquat poisoning using bioinformatics analysis

[Objective] In this study, differentially expressed genes (DEGs) and signaling pathways involved in diquat (DQ) and paraquat (PQ) poisoning were identified via bioinformatics analysis, in order to inform the development of novel clinical treatments. [Methods] Raw data from GSE153959 were downloaded from the Gene Expression Omnibus database. DEGs of the DQ vs. control (CON) and PQ vs. CON comparison groups were identified using R, and DEGs shared by the two groups were identified using TBtools. Subsequently, the shared DEGs were searched in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, using the Database for Annotation, Visualization, and Integrated Discovery. A protein-protein interaction (PPI) network was constructed, and hub genes were identified using the cytoHubba plug-in in Cytoscape software. Finally, Circos and contrast plots showing the DEGs shared between mouse and human chromosomes were constructed using TBtools. [Results] Thirty- one DEGs shared by the DQ and PQ groups were identified. Enriched biological process terms included positive regulation of cell proliferation and translation. Enriched cellular component terms included extracellular region, intracellular membrane- bounded organelle and mitochondrion. Enriched molecular function terms included transcription factor activity and sequence-specific double-stranded DNA binding. Enriched KEGG pathways included the interleukin- 17 signaling pathway, tumor necrosis factor signaling pathway, and human T- cell leukemia virus 1 infection. The top ten hub genes in the PPI network were Ptgs2, Cxcl2, Csf2, Mmp13, Areg, Plaur, Fosl1, Ereg, Atf3, and Tfrc. Cxcl2, Csf2, and Atf3 played important roles in the mitogen- activated protein kinase signaling pathway. [Conclusions] These pathways and DEGs may serve as targets for gene therapy.

Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data

BACKGROUND

Pathway enrichment analysis (PEA) is a well-established methodology for interpreting a list of genes and proteins of interest related to a condition under investigation. This paper aims to extend our previous work in which we introduced a preliminary comparative analysis of pathway enrichment analysis tools. We extended the earlier work by providing more case studies, comparing BiP enrichment performance with other well-known PEA software tools.

METHODS

PEA uses pathway information to discover connections between a list of genes and proteins as well as biological mechanisms, helping researchers to overcome the problem of explaining biological entity lists of interest disconnected from the biological context.

RESULTS

We compared the results of BiP with some existing pathway enrichment analysis tools comprising Centrality-based Pathway Enrichment, pathDIP, and Signaling Pathway Impact Analysis, considering three cancer types (colorectal, endometrial, and thyroid), for a total of six datasets (that is, two datasets per cancer type) obtained from the The Cancer Genome Atlas and Gene Expression Omnibus databases. We measured the similarities between the overlap of the enrichment results obtained using each couple of cancer datasets related to the same cancer.

CONCLUSION

As a result, BiP identified some well-known pathways related to the investigated cancer type, validated by the available literature. We also used the Jaccard and meet-min indices to evaluate the stability and the similarity between the enrichment results obtained from each couple of cancer datasets. The obtained results show that BiP provides more stable enrichment results than other tools.

Nickel and Oxidative Stress: Cell Signaling Mechanisms and Protective Role of Vitamin C

BACKGROUND

Nickel activates the signaling pathways through the oxygen sensing mechanism and the signaling cascades that control hypoxia-inducible transcriptional gene expressions through oxidative stress. This review emphasizes on the recent updates of nickel toxicities on oxidant and antioxidant balance, molecular interaction of nickel and its signal transduction through low oxygen microenvironment in the in-vivo physiological system.

DISCUSSION

Nickel alters intracellular chemical microenvironment by increasing ionized calcium concentration, lipid peroxidation, cyclooxygenase, constitutive nitric oxide synthase, leukotriene B4, prostaglandin E2, interleukins, tumor necrosis factor-α, caspases, complement activation, heat shock protein 70 kDa and hypoxia-inducible factor-1α. The oxidative stress induced by nickel is responsible for the progression of metastasis. It has been observed that nickel exposure induces the generation of reactive oxygen species which leads to the increased expression of p53, NF-kβ, AP-1, and MAPK. Ascorbic acid (vitamin C) prevents lipid peroxidation, oxidation of low-density lipoproteins and advanced oxidation protein products. The mechanism involves that vitamin C is capable of reducing ferric iron to ferrous iron in the duodenum, thus the availability of divalent ferrous ion increases which competes with nickel (a divalent cation itself) and reduces its intestinal absorption and nickel toxicities.

CONCLUSION

Reports suggested the capability of ascorbic acid as a regulatory factor to influence gene expression, apoptosis and other cellular functions of the living system exposed to heavy metals, including nickel.

In the mouse, prostaglandin D2 signalling protects the endometrium against adenomyosis

Adenomyosis is characterised by epithelial gland and mesenchymal stroma invasion of the uterine myometrium. Adenomyosis is an oestrogen-dependent gynaecological disease in which a number of factors, such as inflammatory molecules, prostaglandins (PGs), angiogenic factors, cell proliferation and extracellular matrix remodelling proteins, also play a role as key disease mediators. In this study, we used mice lacking both lipocalin and hematopoietic-PG D synthase (L- and H-Pgds) genes in which PGD2 is not produced to elucidate PGD2 roles in the uterus. Gene expression studied by real-time PCR and hormone dosages performed by ELISA or liquid chromatography tandem mass spectroscopy in mouse uterus samples showed that components of the PGD2 signalling pathway, both PGDS and PGD2-receptors, are expressed in the mouse endometrium throughout the oestrus cycle with some differences among uterine compartments. We showed that PGE2 production and the steroidogenic pathway are dysregulated in the absence of PGD2. Histological analysis of L/H-Pgds-/- uteri, and immunohistochemistry and immunofluorescence analyses of proliferation (Ki67), endothelial cell (CD31), epithelial cell (pan-cytokeratin), myofibroblast (α-SMA) and mesenchymal cell (vimentin) markers, identify that 6-month-old L/H-Pgds-/- animals developed adenomyotic lesions, and that disease severity increased with age. In conclusion, this study suggests that the PGD2 pathway has major roles in the uterus by protecting the endometrium against adenomyosis development. Additional experiments, using for instance transcriptomic approaches, are necessary to fully determine the molecular mechanisms that lead to adenomyosis in L/H-Pgds-/- mice and to confirm whether this strain is an appropriate model for studying the human disease.

Ursolic acid ameliorates Nthy-ori 3-1 cells injury induced by IL-1β through limiting MALAT1/miR-206/PTGS1 ceRNA network and NF-κB signaling pathway

RATIONALE

Ursolic acid (UA) has exhibited anti-inflammatory and anti-oxidative drug effects.

OBJECTIVES

In the research, we assessed the effects of UA on Nthy-ori 3-1 cells stimulated by IL-1β and attempted to elucidate the mechanisms underlying the effects.

METHODS

Autoimmune thyroiditis (AIT) was simulated using Nthy-ori 3-1 cells by IL-1β (10 μM) treatment. UA (20 μM) was applied to ameliorate the injury of Nthy-ori 3-1 cells. The target of UA was predicted by TCMSP, BATMAN, and GEO database. Targeted relationship between lncRNA MALAT1 and miR-206, as well as miR-206 and PTGS1, was predicted by bioinformatics software and identified by dual luciferase assays. Cytokines in the cell supernatant and the apoptosis of cells were detected by ELISAs and flow cytometry assays, respectively. Expression levels of NF-κB signaling pathway-related proteins were estimated by western blot.

RESULTS

By enquiring TCMSP, BATMAN, and GEO database, PTGS1 was identified as a target of UA. Afterward, a ceRNA network among MALAT1, miR-206, and PTGS1 was constructed. The expression levels of MALAT1 and PTGS1 in AIT tissues were obviously enhanced. Moreover, the ceRNA network formed by MALAT1/miR-206/PTGS1 contributed to the damage of Nthy-ori 3-1 cells induced by IL-1β. However, UA ameliorated the Nthy-ori 3-1 cells injury induced by IL-1β through mediating the MALAT1/miR-206/PTGS1 ceRNA network and NF-κB signaling pathway.

CONCLUSIONS

UA treatment significantly relieved the injury of Nthy-ori 3-1 cells via inhibiting the ceRNA mechanism of MALAT1/miR-206/PTGS1 and inflammatory pathways, insinuating that UA may be helpful for the treatment of AIT.

SAMHD1 is a key regulator of the lineage-specific response of acute lymphoblastic leukaemias to nelarabine

The nucleoside analogue nelarabine, the prodrug of arabinosylguanine (AraG), is effective against T-cell acute lymphoblastic leukaemia (T-ALL) but not against B-cell ALL (B-ALL). The underlying mechanisms have remained elusive. Here, data from pharmacogenomics studies and a panel of ALL cell lines reveal an inverse correlation between nelarabine sensitivity and the expression of SAMHD1, which can hydrolyse and inactivate triphosphorylated nucleoside analogues. Lower SAMHD1 abundance is detected in T-ALL than in B-ALL in cell lines and patient-derived leukaemic blasts. Mechanistically, T-ALL cells display increased SAMHD1 promoter methylation without increased global DNA methylation. SAMHD1 depletion sensitises B-ALL cells to AraG, while ectopic SAMHD1 expression in SAMHD1-null T-ALL cells induces AraG resistance. SAMHD1 has a larger impact on nelarabine/AraG than on cytarabine in ALL cells. Opposite effects are observed in acute myeloid leukaemia cells, indicating entity-specific differences. In conclusion, SAMHD1 promoter methylation and, in turn, SAMHD1 expression levels determine ALL cell response to nelarabine.

Genetic Deficiency of the Histamine H4-Receptor Reduces Experimental Colorectal Carcinogenesis in Mice

Colorectal cancer (CRC), a severe complication of inflammatory bowel diseases, is a common type of cancer and accounts for high mortality. CRC can be modeled in mice by application of the tumor promoter, azoxymethane (AOM), in combination with dextran sodium sulfate (DSS), which are able to induce colitis-like manifestations. Active colitis correlates with high mucosal concentrations of histamine, which, together with the histamine receptor subtype 4 (H₄R), provide a pro-inflammatory function in a mouse colitis model. Here, we analyzed whether H₄R is involved in the pathogenesis of AOM/DSS-induced CRC in mice. As compared to wild type (WT) mice, AOM/DSS-treated mice lacking H₄R expression (TM) demonstrate ameliorated signs of CRC, i.e., significantly reduced loss of body weight, stiffer stool consistency, and less severe perianal bleeding. Importantly, numbers and diameters of tumors and the degree of colonic inflammation are dramatically reduced in TM mice as compared to WT mice. This is concomitant with a reduced colonic inflammatory response involving expression of cyclooxygenase 2 and the production of C-X-C motif chemokine ligand 1 (CXCL1) and CXCL2. We conclude that H₄R is involved in the tumorigenesis of chemically-induced CRC in mice via cyclooxygenase 2 expression and, probably, CXCL1 and CXCL2 as effector molecules.

Evaluation of Glycosylated PTGS2 in Colorectal Cancer for NSAIDS-Based Adjuvant Therapy

Observational/retrospective studies indicate that prostaglandin-endoperoxide synthase-2 (PTGS2) inhibitors could positively affect colorectal cancer (CRC) patients' survival after diagnosis. To obtain an acceptable cost/benefit balance, the inclusion of PTGS2 inhibitors in the adjuvant setting needs a selective criterion. We quantified the 72 kDa, CRC-associated, glycosylated form of PTGS2 in 100 frozen CRC specimens and evaluated PTGS2 localization by IHC in the same tumors, scoring tumor epithelial-derived and stroma-derived fractions. We also investigated the involvement of interleukin-1 beta (IL1β) in PTGS2 induction, both in vitro and in CRC lysates. Finally, we used overall survival (OS) as a criterion for patient selection. Glycosylated PTGS2 can be quantified with high sensibility in tissue lysates, but the expression in both tumor and stromal cells limits its use for predictive purposes. Immunohistochemistry (IHC) analysis indicates that stromal PTGS2 expression could exert a protective role on patient OS. Stromal PTGS2 was prevalently expressed by cancer-associated fibroblasts exerting a barrier function near the gut lumen, and it apparently favored the antitumor M1 macrophage population. IL1β was directly linked to gPTGS2 expression both in vitro and in tumors, but its activity was apparently prevalent on the stromal cell population. We suggest that stromal PTGS2 could exert a positive effect on patients OS when expressed in the luminal area of the tumor.