Ligand-receptor Interaction Signaling Pathway Research Articles

Red light-induced localized release of carbon monoxide for alleviating postoperative cognitive dysfunction

Inflammation within the central nervous system (CNS), which may be triggered by surgical trauma, has been implicated as a significant factor contributing to postoperative cognitive dysfunction (POCD). The relationship between mitigating inflammation at peripheral surgical sites and its potential to attenuate the CNS inflammatory response, thereby easing POCD symptoms, remains uncertain. Notably, carbon monoxide (CO), a gasotransmitter, exhibits pronounced anti-inflammatory effects. Herein, we have developed carbon monoxide-releasing micelles (CORMs), a nanoparticle that safely and locally liberates CO upon exposure to 650 nm light irradiation. In a POCD mouse model, treatment with CORMs activated by light (CORMs + hv) markedly reduced the concentrations of interleukin (IL)-6, IL-1β, and tumor necrosis factor-alpha (TNF-α) in both the peripheral blood and the hippocampus, alongside a decrease in ionized calcium-binding adapter molecule 1 in the hippocampal CA1 region. Furthermore, CORMs + hv treatment diminished Evans blue extravasation, augmented the expression of tight junction proteins zonula occludens-1 and occludin, enhanced neurocognitive functions, and fostered fracture healing. Bioinformatics analysis and experimental validation has identified Htr1b and Trhr as potential key regulators in the neuroactive ligand-receptor interaction signaling pathway implicated in POCD. This work offers new perspectives on the mechanisms driving POCD and avenues for therapeutic intervention.

Molecular mechanisms of quetiapine bidirectional regulation of bipolar depression and mania based on network pharmacology and molecular docking: Evidence from computational biology

BackgroundQuetiapine monotherapy is recommended as the first-line option for acute mania and acute bipolar depression. However, the mechanism of action of quetiapine is unclear. Network pharmacology and molecular docking were employed to determine the molecular mechanisms of quetiapine bidirectional regulation of bipolar depression and mania. MethodsPutative target genes for quetiapine were collected from the GeneCard, SwissTargetPrediction, and DrugBank databases. Targets for bipolar depression and bipolar mania were identified from the DisGeNET and GeneCards databases. A protein-protein interaction (PPI) network was generated using the String database and imported into Cytoscape. DAVID and the Bioinformatics platform were employed to perform the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the top 15 core targets. The drug-pathway-target-disease network was constructed using Cytoscape. Finally, molecular docking was performed to evaluate the interactions between quetiapine and potential targets. ResultsTargets for quetiapine actions against bipolar depression (126 targets) and bipolar mania (81 targets) were identified. Based on PPI and KEGG pathway analyses, quetiapine may affect bipolar depression by targeting the MAPK and PI3K/AKT insulin signaling pathways via BDNF, INS, EGFR, IGF1, and NGF, and it may affect bipolar mania by targeting the neuroactive ligand-receptor interaction signaling pathway via HTR1A, HTR1B, HTR2A, DRD2, and GRIN2B. Molecular docking revealed good binding affinity between quetiapine and potential targets. LimitationsPharmacological experiments should be conducted to verify and further explore these results. ConclusionsOur findings suggest that quetiapine affects bipolar depression and bipolar mania through distinct biological core targets, and thus through different mechanisms. Furthermore, our results provide a theoretical basis for the clinical use of quetiapine and possible directions for new drug development.

Influence of Heat Treatment on Tea Polyphenols and Their Impact on Improving Heat Tolerance in Drosophila melanogaster.

This study investigated the potential mechanism of action of tea polyphenols (TPs), one of the major active ingredients in tea, to enhance heat resistance in Drosophila and the attenuating effect of heat treatment of TPs on their efficacy. The results showed that TPs were able to prolong the average survival time of Drosophila under high-temperature stress (p < 0.05), but the effect of TPs in prolonging the survival time of Drosophila melanogaster was significantly reduced (p < 0.05) with increasing TP heat-treatment time until it disappeared. The composition of TPs changed after heat treatment. It was also shown that the weakening of the effect of TPs in improving the heat tolerance of Drosophila was related to the decrease in the content of catechins and phenolic acids in their fractions as well as with the increase in the content of laccase. Transcriptomic analysis showed that the effect of TPs on heat tolerance in Drosophila melanogaster was closely related to the longevity regulation pathway, the neuroactive ligand-receptor interaction signaling pathway, and the drug metabolism-cytochrome P450 pathway. Metabolomics analysis showed that the effect of TP intervention in improving the body's heat tolerance was mainly related to amino acid metabolism and energy metabolism. However, thermal processing weakened the relevance of these transcriptomes and metabolomes. The present study reveals the mechanism of action by which heat-treated TPs affect the body's heat tolerance, which is important for the development and utilization of the heat-protection function of tea.

Preliminary study on toxicological mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to cd

BackgroundCadmium (Cd) flows into the ocean with industrial and agricultural pollution and significantly affects the growth and development of economic cephalopods such as Sepia esculenta, Amphioctopus fangsiao, and Loligo japonica. As of now, the reasons why Cd affects the growth and development of S. esculenta are not yet clear.ResultsIn this study, transcriptome and four oxidation and toxicity indicators are used to analyze the toxicological mechanism of Cd-exposed S. esculenta larvae. Indicator results indicate that Cd induces oxidative stress and metal toxicity. Functional enrichment analysis results suggest that larval ion transport, cell adhesion, and some digestion and absorption processes are inhibited, and the cell function is damaged. Comprehensive analysis of protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to explore S. esculenta larval toxicological mechanisms, and we find that among the 20 identified key genes, 14 genes are associated with neurotoxicity. Most of them are down-regulated and enriched to the neuroactive ligand-receptor interaction signaling pathway, suggesting that larval nervous system might be destroyed, and the growth, development, and movement process are significantly affected after Cd exposure.ConclusionsS. esculenta larvae suffered severe oxidative damage after Cd exposure, which may inhibit digestion and absorption functions, and disrupt the stability of the nervous system. Our results lay a function for understanding larval toxicological mechanisms exposed to heavy metals, promoting the development of invertebrate environmental toxicology, and providing theoretical support for S. esculenta artificial culture.

Evaluation of developmental toxicity of safinamide in zebrafish larvae (Danio rerio)

Monoamine oxidase-B (MAO-B), as a principal metabolizing enzyme, plays important roles in the metabolism of catecholamines and xenobiotics in the central nervous system and peripheral tissues. Safinamide, the third-generation reversible MAO-B inhibitor, has potential to alleviate many neurological diseases such as Parkinson's disease (PD) and depression. Exposure to clinical psychotropic drugs often has adverse effects on fetuses. Currently, a variety of studies of safinamide focus on its curative effect and pharmacological effect, while its side effect of embryonic development is barely studied. In this study, we used zebrafish as a model to evaluate the embryonic developmental toxicity of safinamide. Our results revealed that higher concentrations (30 μM) of safinamide treatment caused a decrease in hatching rate and an increase in malformation and mortality in zebrafish larvae. Meanwhile, we observed that lower safinamide exposure (10 μM) increased the body length of zebrafish larvae and resulted in hyperactivity-like behaviors. In addition, an increased trend in dopamine (DA) level was found in 3.3 μM and 10 μM safinamide-exposed groups. Transcriptome analysis identified that safinamide exposure may disturb a variety of physiological processes such as neuroactive ligand-receptor interaction signaling pathway. In summary, our study reveals that safinamide may cause developmental defects in zebrafish larvae and provides insights into its toxic reactions in early develoment.

Transcriptome Analysis of the Mouse Medial Prefrontal Cortex in a Chronic Constriction Injury Model.

The medial prefrontal cortex (mPFC) is critical for both the sensory and emotional/cognitive components of pain. However, the underlying mechanism remains largely unknown. Here, we examined changes in the transcriptomic profiles in the mPFC of mice with chronic pain using RNA sequencing (RNA-seq) technology. A mouse model of peripheral neuropathic pain was established via chronic constriction injury (CCI) of the sciatic nerve. CCI mice developed sustained mechanical allodynia and thermal hyperalgesia, as well as cognitive impairment four weeks after surgery. RNA-seq was conducted 4weeks after CCI surgery. Compared with contral group, RNA-seq identified a total 309 and 222 differentially expressed genes (DEGs) in the ipsilateral and contralateral mPFC of CCI model mice, respectively. GO analysis indicated that the functions of these genes were mainly enriched in immune- and inflammation-related processes such as interferon-gamma production and cytokine secretion. KEGG analysis further showed the enrichment of genes involved in the neuroactive ligand-receptor interaction signaling pathway and Parkinson disease pathway that have been reported to be importantly involved in chronic neuralgia and cognitive dysfunction. Our study may provide insights into the possible mechanisms underlying neuropathic pain and pain-related comorbidities.

Isopropyl 3-(3,4-dihydroxyphenyl)-2-hydroxypropanoate plays an anti-hypoxic role through regulating neuroactive ligand-receptor interaction signaling pathway in larval zebrafish

Isopropyl 3-(3,4-dihydroxyphenyl)-2-hydroxypropanoate (IDHP) is the core active substance of salvia miltiorrhiza in disease treatment. The significance of our work lies in evaluating the ameliorating effects of IDHP on hypoxia-induced injury and investigating its mechanisms. We examined the morphology, dopamine neurons (DANs), cerebral vessels, and behavior of zebrafish larvae administrated by IDHP/VHC after hypoxia-induction. We next sought to explore its anti-hypoxic mechanisms via transcriptome analysis and qPCR experiments. The results indicated that hypoxia-induced injuries, including decreased length of DANs, number of cereal vessels, total swimming distance, and average swimming speed, were all alleviated by IDHP. Furthermore, transcriptome analysis provided a sign that IDHP most likely played the anti-hypoxic role through the neuroactive ligand-receptor interaction (NLRI) signaling pathway. Consistently, expression of related genes, such as f2rl1.1, p2ry10, npy1r, ptger2b, ptger2b, pth2rb, and nmur1a, was downregulated by hypoxia induction and recovered after IDHP administration. Therefore, we speculated that, via regulating NLRI, IDHP reduced inflammation, promoted angiogenesis, modulated blood pressure and flow, and inhibited cell apoptosis, and eventually played an anti-hypoxic role.

Study on the Potential Mechanism of Semen Strychni against Myasthenia Gravis Based on Network Pharmacology and Molecular Docking with Experimental Verification.

Background Semen Strychni (SS) is an effective Chinese medicine formula for treating myasthenia gravis (MG) in clinics. Nonetheless, its molecular mechanism is largely unknown. Objective Using network pharmacology, molecular docking, and experimental validation, we aim to identify the therapeutic effect of SS on MG and its underlying mechanism. Methods The main ingredients of SS and their targets and potential disease targets for MG were extracted from public databases. The protein-protein interaction (PPI) network was constructed using the STRING 11.0 database, and Cytoscape was used to identify the hub targets. In addition, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify molecular biological processes and signaling pathways. Then, AutoDock Via conducted molecular docking. The experimental autoimmune myasthenia gravis (EAMG) model in female Lewis rats, quantitative real-time polymerase chain reaction (qRT-PCR), Western blot, and enzyme-linked immunosorbent assay (ELISA) were performed to confirm the effect and mechanism of SS on MG. Results The following active compounds and hub targets were identified by screening and analyzing: isobrucine, vomicine, (S)-stylopine, strychnine, brucine-N-oxide, brucine and AKT1, MAPK1, MAPK14, CHRM1, ACHE, and CHRNA4. KEGG enrichment analyses indicated that the cholinergic synapse and neuroactive ligand-receptor interaction signaling pathway may be necessary. The results of molecular docking revealed that the main active ingredients bind well to the hub targets. In vivo experiments proved that SS could improve the weight loss and Lennon scores in the EAMG model. Experiments in molecular biology showed that SS could treat MG by affecting the cholinergic synapse through the respective antibody, receptor, and key enzymes in the cholinergic pathway. Conclusion This study provided a preliminary overview of the active constituents, primary targets, and potential pathways of SS against MG. SS ameliorated EAMG by regulating the cholinergic synaptic junction.

Antidepressant effect and molecular mechanism of notoginsenoside R_1 based on network pharmacology and animal experiments

To provide experimental basis and theoretical guidance for further research on the molecular mechanism of notoginsenoside R_1(NGR_1) in the treatment of depression, the present study analyzed the potential mechanism of NGR_1 in the treatment of depression through network pharmacology and verified it by molecular docking and animal experiments. PharmMapper, SwissTargetPrediction, and GeneCards were used to predict the related targets of both NGR_1 and depression to obtain the potential targets of NGR_1 in the treatment of depression. The database for annotation, visualization and integrated discovery(DAVID) was used for GO functional annotation and KEGG pathway enrichment analysis to screen the possible mechanisms of NGR_1 exerting antidepressant effect. Cytoscape 3.9.0 was adopted to construct a protein-protein interaction(PPI) network, and the topological analysis was performed to obtain the core targets. The binding activity of NGR_1 to core targets was tested by molecular docking. The depression model was prepared by injecting lipopolysaccharide(LPS) into the lateral ventricle in mice, and intervened with NGR_1. The antidepressant effect of NGR_1 was detected by behavioral tests and RT-qPCR. The results showed that by network pharmacology, 56 common targets of NGR_1 and depression were predicted, and GO enrichment analysis determined 13 related biological processes, mainly involving G protein-coupled receptor signaling pathway, positive regulation of transcription from RNA polymerase Ⅱ promoter, cytokine-mediated signaling pathway, gene expression, apoptosis, cell proliferation, and signal transduction. In addition, KEGG pathway enrichment analysis identified ten potential pathways, including neuroactive ligand-receptor interaction signaling pathway, lipid and atherosclerosis signaling pathway, cAMP signaling pathway, PI3 K-AKT signaling pathway, and lipid and atherosclerosis signaling pathway. PPI analysis revealed that the core targets included CASP3, VEGFA, IGF1, STAT3, MAPK1, PPARG, MTOR, MAPK14, NR3 C1 and AR, and molecular docking demonstrated that NGR_1 had desirable binding activity to these target proteins. In animal experiments, the results showed that NGR_1 improved the disease behavior of depressed mice, significantly inhibited the neuroinflammatory response(reducing the mRNA expression of Iba-1, TNF-α, IL-1β, and IL-6), and regulated the mRNA expression of lipid and atherosclerosis signaling pathway-related targets(CASP3, STAT3, MAPK1 and MAPK14). This indicated that the antidepressant mechanism of NGR_1 may be related to the regulation of lipid and atherosclerosis signaling pathway. In conclusion, network pharmacology was used to reveal the core targets and pathways of NGR_1, and some of them were verified in animal experiments, which provided the basis for in-depth exploration on the mechanism of NGR_1 in the treatment of depression.

Network Pharmacology and Molecular Docking Analysis on Molecular Targets and Mechanisms of "Chuanxiong Rhizoma: Radix Salviae miltiorrhizae" Herb Couples in the Treatment of Preeclampsia.

Objective The aim of the study is to explore the molecular mechanism of activating blood circulation and dispersing stasis herbs in the treatment of pre-eclampsia with Chuanxiong Rhizoma-Radix Salvia miltiorrhiza. Methods The chemical composition and targets of Chuanxiong Rhizoma-Radix Salvia miltiorrhiza were retrieved from the TCMSP database, and a PPI network was constructed for common genes. Subsequently, a graph of the “active component-target-action pathway” was plotted by Cytoscape 3.7.2 and a KEGG pathway enrichment was performed using the R language cluster profiler package. Molecular docking was conducted between the top five PPI targets of Chuanxiong Rhizoma-Radix Salvia miltiorrhiza. Results According to network pharmacology, there were 32 target genes, 60 active components, and 59 pathways in Chuanxiong Rhizoma-Radix Salvia miltiorrhiza, and its most evident effects were exerted on G-protein-coupled amine receptors and the neuroactive ligand-receptor interaction signaling pathway. Molecular docking indicated that the target protein had a good binding ability with the drugs. Conclusion Chuanxiong Rhizoma-Radix Salvia miltiorrhiza have therapeutic effects in pre-eclampsia, as confirmed by the results of molecular biology analysis. Thus, the Chuanxiong Rhizoma-Radix Salvia miltiorrhiza regimen provides a basis for the treatment of pre-eclampsia using traditional Chinese medicine.

Screening and Biological Function Analysis of miRNA and mRNA Related to Lung Adenocarcinoma Based on Bioinformatics Technology.

Objective To screen the differentially expressed miRNAs (DEMs) and the differentially expressed gene mRNAs (DEGs) in lung adenocarcinoma (LUAD) from the TCGA database and to explore the relationship between miRNAs and the prognosis of lung adenocarcinoma and their biological functions. Methods The RNA-seq and miRNA-seq data of lung adenocarcinoma samples were downloaded from the TCGA database for analysis, and the R program was used to screen for differentially expressed miRNAs and mRNAs. Then, the molecular functions, biological processes, cellular components, and signaling pathways involved in the occurrence and development of LUAD were analyzed using the functional accumulation analysis software of GSEA. The relationship between the integrated differentially expressed RNAs was analyzed by miRcode, TargetScan, and miRTarbase databases, and the miRNA-mRNA network was constructed. Result A total of 516 differentially expressed miRNAs and 5464 differentially expressed mRNAs were identified in LUAD. The GSEA enrichment analysis showed that miRNAs and mRNAs were mainly enriched in extracellular structure organization, external encapsulating structure organization, extracellular matrix organization, and gated channel activity. They were mainly involved in neuroactive ligand-receptor interaction signaling pathway. Some miRNAs and mRNAs in clustering modules were found to be associated with the prognosis of LUAD. Four targeting networks consisting of 22 miRNAs and 531 mRNAs were constructed. Conclusion The miRNA and mRNA related to the prognosis of LUAD were screened out, which provided a valuable preliminary basis for the follow-upin-depth clinical research and basic experimental research of LUAD.

Antiepileptic Therapy of Abrus cantoniensis: Evidence from Network Pharmacology.

The present study explores the mechanism of antiepileptic treatment of Abrus cantoniensis through network pharmacology. During this process, several databases were recruited, e.g., the TCMSP database, HERB database, and SwissTargetPrediction database were used to retrieve the active components and targets of Abrus cantoniensis; GeneCards database and OMIM database were used to retrieve the targets of epilepsy. The targets of epilepsy and Abrus cantoniensis were subjected to target intersection in venny2.1, and protein interaction analysis of Abrus cantoniensis in the String database. We set the Cyto NCA plug-in condition as betweenness; selected the first 8 genes of betweenness as the core genes; performed the integrative bioinformatics of candidates by GO analysis and KEGG analysis. Moreover, AutoDockTools and AutoDockVina software were used to perform the molecular docking; Pymol was used to perform the docking visualization. We obtained three active components of Abrus cantoniensis, which are mainly related to β-sitosterol and stigmasterol; 92 intersection targets of epilepsy of Abrus cantoniensis, including 9 core targets such as AKT1, ESR1, MMP9, CES1, SRC, HIF1A, ABCB1, CASP3, and SNCA; 8 core targets were flavanone constituent proteins. Define p value less than 0.05; according to the screening principle, the first 20 GO pathways and KEGG pathways were selected. We found that Abrus cantoniensis was mainly connected with epilepsy through the neuroactive ligand-receptor interaction signaling pathway, the neurodegeneration pathway, and multiple disease signaling pathway; the docking between ESR1 and components is the most stable among the core targets. Besides, the binding energies of the core targets were all less than −5 kcal mol−1. Taken together, the current research provides a new strategy for the antiepileptic treatment of Abrus cantoniensis.

Analysis of transcriptome characteristics of UTI therapy for cerebral injury after CA/ROSC based on RNA-seq technique.

Objective(s):To study the effects and mechanisms of ulinastatin (UTI) on brain injury caused by cardiac arrest/return of spontaneous circulation (CA/ROSC). Materials and Methods:In this study, modeling of CA/ROSC was set up in 56 Sprague Dawley (SD) rats, which were randomly divided into the model group, UTI (100000U/kg) treatment group, and control group. Each group then was divided into two subgroups: 24 hr and 72 hr. The survival rates between different groups was observed during two weeks. AimPlex multiplex immunoassays technology was performed to detect the expression of inflammatory cytokines in serum, such as IL-6 and TNF-α. RNA-sequencing (RNA-seq) transcriptome, Gene Ontology (GO), and Kyoto. Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to investigate the possible mechanism of UTI. Western blot and immunohistochemistry were performed to detect the expression of C-C motif chemokine ligand 2 (CCl2) and plasminogen (plg) protein expression.Results:The survival rate of the UTI group was significantly higher than the model group during two weeks. And UTI can significantly reduce the content of IL-6 and TNF-α in serum. GO and KEGG pathway enrichment analysis revealed that differentially expressed genes mainly belonged to the IL-17 signaling pathway and neuroactive ligand-receptor interaction signaling pathway. Besides, UTI can down-regulate the expression of the CCl2 inflammatory gene and up-regulate the expression of plg in the brain tissue of CA/ROSC rats. Conclusion:UTI has neuroprotective effects on brain injury after CA/ROSC. And the key mechanisms belong to the regulation of immune-inflammatory response as well as the signaling molecules and interaction.

Research progress of Curcuma kwangsiensis root tubers and analysis of liver protection and anti-tumor mechanisms based on Q-markers

Curcuma kwangsiensis root tuber is a widely used genuine medicinal material in Guangxi, with the main active components of terpenoids and curcumins. It has the effects of promoting blood circulation to relieve pain, moving Qi to relieve depression, clearing heart and cooling blood, promoting gallbladder function and anti-icterus. Modern research has proved its functions in liver protection, anti-tumor, anti-oxidation, blood lipid reduction and immunosuppression. Considering the research progress of C. kwangsiensis root tubers and the core concept of quality marker(Q-marker), we predicted the Q-markers of C. kwangsiensis root tubers from plant phylogeny, chemical component specificity, traditional pharmacodynamic properties, new pharmacodynamic uses, chemical component measurability, processing methods, compatibility, and components migrating to blood. Curcumin, curcumol, curcumadiol, curcumenol, curdione, germacrone, and β-elemene may be the possible Q-markers. Based on the predicted Q-markers, the mechanisms of the liver-protecting and anti-tumor activities of C. kwangsiensis root tubers were analyzed. AKT1, IL6, EGFR, and STAT3 were identified as the key targets, and neuroactive ligand-receptor interaction signaling pathway, nitrogen metabolism pathway, cancer pathway, and hepatitis B pathway were the major involved pathways. This review provides a basis for the quality evaluation and product development of C. kwangsiensis root tubers and gives insights into the research on Chinese medicinal materials.

Molecular Mechanism of Gelsemium elegans (Gardner and Champ.) Benth. Against Neuropathic Pain Based on Network Pharmacology and Experimental Evidence.

Gelsemium elegans (Gardner and Champ.) Benth. (Gelsemiaceae) (GEB) is a toxic plant indigenous to Southeast Asia especially China, and has long been used as Chinese folk medicine for the treatment of various types of pain, including neuropathic pain (NPP). Nevertheless, limited data are available on the understanding of the interactions between ingredients-targets-pathways. The present study integrated network pharmacology and experimental evidence to decipher molecular mechanisms of GEB against NPP. The candidate ingredients of GEB were collected from the published literature and online databases. Potentially active targets of GEB were predicted using the SwissTargetPrediction database. NPP-associated targets were retrieved from GeneCards, Therapeutic Target database, and DrugBank. Then the protein-protein interaction network was constructed. The DAVID database was applied to Gene Ontology and Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis. Molecular docking was employed to validate the interaction between ingredients and targets. Subsequently, a 50 ns molecular dynamics simulation was performed to analyze the conformational stability of the protein-ligand complex. Furthermore, the potential anti-NPP mechanisms of GEB were evaluated in the rat chronic constriction injury model. A total of 47 alkaloids and 52 core targets were successfully identified for GEB in the treatment of NPP. Functional enrichment analysis showed that GEB was mainly involved in phosphorylation reactions and nitric oxide synthesis processes. It also participated in 73 pathways in the pathogenesis of NPP, including the neuroactive ligand-receptor interaction signaling pathway, calcium signaling pathway, and MAPK signaling pathway. Interestingly, 11-Hydroxyrankinidin well matched the active pockets of crucial targets, such as EGFR, JAK1, and AKT1. The 11-hydroxyrankinidin-EGFR complex was stable throughout the entire molecular dynamics simulation. Besides, the expression of EGFR and JAK1 could be regulated by koumine to achieve the anti-NPP action. These findings revealed the complex network relationship of GEB in the “multi-ingredient, multi-target, multi-pathway” mode, and explained the synergistic regulatory effect of each complex ingredient of GEB based on the holistic view of traditional Chinese medicine. The present study would provide a scientific approach and strategy for further studies of GEB in the treatment of NPP in the future.

Long Non-coding RNAs Gabarapl2 and Chrnb2 Positively Regulate Inflammatory Signaling in a Mouse Model of Dry Eye.

Purpose: To elucidate the expression profile and the potential role of long non-coding ribonucleic acids (RNAs) (lncRNAs) in a dry eye disease (DED) model.Methods: A DED model was established in C57BL/6J mice with 0.2% benzalkonium chloride (BAC) twice a day for 14 days. The differentially expressed lncRNAs were detected by RNA-seq technology (Gene Expression Omnibus, GEO GSE186450) and the aberrantly expressed lncRNAs were further verified by RT-qPCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to predicate the related candidate genes and potential pathological pathways. Cells from a human corneal epithelial cell line (HCECs) were cultured under hyperosmolarity. The regulation of inflammatory factors by silencing potential targeted lncRNAs was verified in vitro in HCECs.Results: In our study, a significant increase in corneal fluorescence staining and a reduction in tear production were observed in DED mice at all follow-ups compared with the controls, and the differences were increasing over time. In total, 2,649 upregulated and 704 downregulated lncRNAs were identified in DED mice. We selected six aberrantly expressed and most abundant lncRNAs and performed RT-qPCR using the samples for RNA-seq. Chrnb2, Gabarapl2, and Usp31 were thereby confirmed as the most significantly altered lncRNAs. Pathway analysis revealed that the neuroactive ligand–receptor interaction signaling pathway was the most enriched, followed by the calcium signaling pathway and cytokine–cytokine receptor interaction. Following treatment of Gabarapl2 siRNA and Chrnb2 siRNA, tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, and IL-6 were significantly downregulated in the HCECs.Conclusion: Our study suggests that Chrnb2 and Gabarapl2 may be involved in the inflammation response by regulating TNF-α, IL-1β, and IL-6 in DED. These candidate lncRNAs may be both potential biomarkers and therapeutic targets for DED.

Low-Dose Exposure of Silica Nanoparticles Induces Neurotoxicity via Neuroactive Ligand-Receptor Interaction Signaling Pathway in Zebrafish Embryos.

ObjectiveSilica nanoparticles (SiO2 NPs) have been extensively employed in biomedical field. SiO2 NPs are primarily designed to enter the circulatory system; however, little information is available on potential adverse effects of SiO2 NPs on the nervous system.MethodsThe neurotoxicity of SiO2 NPs at different concentrations (3, 6, 12 ng/nL) on zebrafish embryos was determined using immunofluorescence and microarray techniques, and subsequently confirmed by qRT-PCR.ResultsSiO2 NPs disrupt the axonal integrity and decrease the length of axons in Tg (NBT: EGFP) transgenic lines. The number of apoptotic cells in the brain and central nervous system of zebrafish embryos was increased in the presence of 12 ng/nL of SiO2 NPs, but the difference did not reach statistical significance. Screening for changes in the expression of genes involved in the neuroactive ligand–receptor interaction pathway was performed by microarray and confirmed by qRT-PCR. These analyses demonstrated that SiO2 NPs markedly downregulated genes associated with neural function (grm6a, drd1b, chrnb3b, adrb2a, grin2ab, npffr2.1, npy8br, gabrd, chrma3, gabrg3, gria3a, grm1a, adra2b, and glra3).ConclusionThe obtained results documented that SiO2 NPs can induce developmental neurotoxicity by affecting the neuroactive ligand–receptor interaction signaling pathway. This new evidence may help to clarify the mechanism of SiO2 NPs-mediated neurotoxicity.

Heterogeneity Analysis of Esophageal Squamous Cell Carcinoma for Precision Oncology Research

Background: Esophageal Squamous Cell Carcinoma (ESCC), which is the most common pathohistological type of esophageal cancer that accounts for roughly 90% of the 456,000 incidents of esophageal cancer cases each year, is a serious malignant disease, with a 15-20% 5-year survival rate worldwide. The outcome of the current established therapeutics for ESCC are not satisfactory. Heterogeneity, including not only the intratumor heterogeneity and complex micro-environment, but also the diversity of heterogeneity across different ESCC samples, is a major biological feature of cancer that is responsible for the establishment of drug resistance and morbidity. Therefore, the diversity of distinct genotypes and phenotypes contributing to this phenomenon should be analyzed for the purpose of precision research and better understanding of ESCC. Methods: Bioinformatic analysis of multi-omics data from The Cancer Cell Line Encyclopedia (CCLE), The Cancer Genome Atlas (TCGA), and Protein Atlas were conducted to investigate heterogeneity across different ESCC samples. Venn Diagrams were utilized to overlap shared and disparate regions of interest between data platforms. DAVID was used for joint functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathways enrichment. The Cytoscape open source software platform and the STRING database were used for integrating and visualizing complex networks with attribute data. Mutation and expression heterogeneity profiles of CCLE-ESCC and TCGA-ESCC samples were analyzed according to matching dissimilarity and correlation distance, respectively. Findings: Heterogeneity at the level of both gene expression and genomic mutations are widespread in the ESCC tumor tissues and established cell lines. In the analysis of animal model data, we observed that there is ambiguity with regards to the source of nearly 50% of identified proteins, which may indicate the existence of trans-species heterogeneity. Our research also indicate that substantial variability exists between different platforms after overlapping sequencing data from cell lines, tumor tissues, normal tissues and PDX tissues of ESCC . Furthermore, Olfactory transduction and Neuroactive ligand-receptor interaction signaling pathways, enriched from the TCGA-ESCC unique proteins, are originally reported in ESCC. Interpretation: Our research found that extensive mutation heterogeneity exists across the samples of ESCC patients and cell lines. The uniquely expressed proteins and relevant signaling pathways provide potential targets for the investigation of carcinogenesis and progression of ESCC. The identification and characterization of genotype and phenotype heterogeneity across different ESCC samples and platforms is essential for developing precise therapeutics for ESCC patients. Funding Statement: This work was supported by National Natural Science Foundation China (NSFC) [No.81872335], Henan Joint Fund [No.U1804196] and Henan Key Science and Technology Program [161100510300]. Declaration of Interests: The authors have no conflict of interest to declare.

Identifying Signatures of Selection Related to Comb Development.

The aim of this study was to identify genes involved in comb development to provide insights into the molecular mechanism of chickens' comb formation. Fixation index (FST) and average number of base differences (π) of males with large and small combs were calculated based on whole-genome resequencing data. Chromosome regions with larger FST values and smaller π were considered candidate selection regions. Through further annotation of gene functions and pathways, we sought to screen possible selected genes associated with comb development. By screening whole genome resequencing data, FST and π were calculated using a 40 Kb sliding window strategy and eight regions were identified. Quantitative trait loci (QTL; FOX1 gene) related to comb length were found on chromosome 1. QTL (GLP1R, BTBD9, MIR6633, and MDGA1 genes) related to comb weight were found on chromosome 3. QTL (ALDH1A1, TMC1, and ANXA1 genes) associated with comb area were found on the Z chromosome. Nineteen genes, Wnt signaling pathway and neuroactive ligand-receptor interaction signaling pathway directly or indirectly related to comb growth and development were found through functional annotation and GO analysis. Among the selected genes LYN, GLP1R, FOX1, TBK1, STRAP, ST6GALNAC, and Wnt signaling pathways were related to immunity. MDGA1, BTBD9, MTSS1, SrGAPs, and neuroactive ligand receptor interaction signaling pathways related to neural function were screened. ALDH1A1, ANXAl, THBS, HIF-1α, and ACTN1 genes were related to heat dissipation. Among the selected genes FOX1, MDGAl, and ANXAl associated with immunity, neurological function, and heat dissipation function coincided with genes affecting the length, weight, and area of the comb. Comprehensive analysis suggested that comb development was due to multiple genes and signaling pathways.

Transcriptomic analysis of \u03b1-synuclein knockdown after T3 spinal cord injury in rats

BackgroundEndogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on transcriptional levels after SCI and to determine the mechanisms underlying α-Syn activity based on RNA-seq.ResultThe establishment of a rat model of lentiviral vector-mediated knockdown of α-Syn in Sprague-Dawley rats with T3 spinal cord contusion (LV_SCI group). The results of the RNA-seq analysis showed that there were 337 differentially expressed genes (DEGs) between the SCI group and the LV_SCI group, and 153 DEGs specific to LV_SCI between the (SCI vs LV_SCI) and (SCI vs CON) comparisons. The top 20 biological transition terms were identified by Gene ontology (GO) analysis. The Kyoto Gene and Genomic Encyclopedia (KEGG) analysis showed that the LV_SCI group significantly upregulated the cholinergic synaptic & nicotine addiction and the neuroactive ligand receptor interaction signaling pathway. Enriched chord analysis analyzes key genes. Further cluster analysis, gene and protein interaction network analysis and RT-qPCR results showed that Chrm2 and Chrnb2 together significantly in both pathways. The proliferation of muscarinic cholinergic receptor subtype 2 (Chrm2) and nicotinic cholinergic receptor subtype β2 (Chrnb2), and the neurogenesis were elevated in the injury site of LV_SCI group by immunofluorescence. Further by subcellular localization, the LV_SCI group enhanced the expression of Chrnb2 at the cell membrane.ConclusionKnockdown of α-Syn after SCI enhance motor function and promote neurogenesis probably through enhancing cholinergic signaling pathways and neuroreceptor interactions. This study not only further clarifies the understanding of the mechanism of knockdown of α-Syn on SCI but also helps to guide the treatment strategy for SCI.