Forsythoside B, the active component of Frosythiae fructuse water extract, alleviates Streptococcus pneumoniae virulence by targeting pneumolysin.

AIMS: To explore the therapeutic potential of Forsythoside B in treating Streptococcus pneumoniae (S. pneumoniae) infections, focusing on its ability to inhibit pneumolysin activity and protect cells from damage. METHODS AND RESULTS: Hemolysis tests were used to evaluate Forsythoside B's inhibitory effect on pneumolysin activity, while growth curve analysis assessed its impact on S. pneumoniae growth. Western blotting and oligomerization analysis were conducted to examine its influence on pneumolysin oligomerization. Cytotoxicity assays, including LDH release and live/dead cell staining, evaluated the protective effects of Forsythoside B against pneumolysin-induced damage in A549 cells. Additionally, a mouse model was employed to test the effects on survival rates, lung bacterial load, and inflammation. The results showed that Forsythoside B significantly inhibited pneumolysin activity, reduced its oligomerization, and protected A549 cells from damage without affecting bacterial growth. In the mouse model, it improved survival rates and reduced lung inflammation, indicating its potential as a therapeutic agent against S. pneumoniae infections. CONCLUSIONS: Forsythoside B shows potential as a therapeutic agent for treating pneumonia, particularly in infections caused by S. pneumoniae.

Wogonin attenuates the pathogenicity of Streptococcus pneumoniae by double-target inhibition of Pneumolysin and Sortase A.

Streptococcus pneumoniae (S. pneumoniae) is a major causative agent of respiratory disease in patients and can cause respiratory distress and other symptoms in severe cases. Pneumolysin (PLY) is a pore-forming toxin that induces host tissue injury and inflammatory responses. Sortase A (SrtA), a catalytic enzyme that anchors surface-associated virulence factors, is critical for S. pneumoniae virulence. Here, we found that the active ingredient of the Chinese herb Scutellaria baicalensis, wogonin, simultaneously inhibited the haemolytic activity of PLY and SrtA activity. Consequently, wogonin decreased PLY-mediated cell damage and reduced SrtA-mediated biofilm formation by S. pneumoniae. Furthermore, our data indicated that wogonin did not affect PLY expression but directly altered its oligomerization, leading to reduced activity. Furthermore, the analysis of a mouse pneumonia model further revealed that wogonin reduced mortality in mice infected with S. pneumoniae laboratory strain D39 and S. pneumoniae clinical isolate E1, reduced the number of colony-forming units in infected mice and decreased the W/D ratio and levels of the inflammatory factors TNF-α, IL-6 and IL-1ß in the lungs of infected mice. Thus, wogonin reduces S. pneumoniae pathogenicity by inhibiting the dual targets PLY and SrtA, providing a treatment option for S. pneumoniae infection.

MMiRNA-Viewer2, a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network.

BACKGROUND: Although there are many studies on the characteristics of miRNA-mRNA interactions using miRNA and mRNA sequencing data, the complexity of the change of the correlation coefficients and expression values of the miRNA-mRNA pairs between tumor and normal samples is still not resolved, and this hinders the potential clinical applications. There is an urgent need to develop innovative methodologies and tools that can characterize and visualize functional consequences of cancer risk gene and miRNA pairs while analyzing the tumor and normal samples simultaneously. RESULTS: We developed an innovative bioinformatics tool for visualizing functional annotation of miRNA-mRNA pairs in a network, known as MMiRNA-Viewer2. The tool takes mRNA and miRNA interaction pairs and visualizes mRNA and miRNA regulation network. Moreover, our MMiRNA-Viewer2 web server integrates and displays the mRNA and miRNA gene annotation information, signaling cascade pathways and direct cancer association between miRNAs and mRNAs. Functional annotation and gene regulatory information can be directly retrieved from our web server, which can help users quickly identify significant interaction sub-network and report possible disease or cancer association. The tool can identify pivotal miRNAs or mRNAs that contribute to the complexity of cancer, while engaging modern next-generation sequencing technology to analyze the tumor and normal samples concurrently. We compared our tools with other visualization tools. CONCLUSION: Our MMiRNA-Viewer2 serves as a multitasking platform in which users can identify significant interaction clusters and retrieve functional and cancer-associated information for miRNA-mRNA pairs between tumor and normal samples. Our tool is applicable across a range of diseases and cancers and has advantages over existing tools.

Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions.

MOTIVATION: Accurate and wide-ranging prediction of thermodynamic parameters for biochemical reactions can facilitate deeper insights into the workings and the design of metabolic systems. RESULTS: Here, we introduce a machine learning method with chemical fingerprint-based features for the prediction of the Gibbs free energy of biochemical reactions. From a large pool of 2D fingerprint-based features, this method systematically selects a small number of relevant ones and uses them to construct a regularized linear model. Since a manual selection of 2D structure-based features can be a tedious and time-consuming task, requiring expert knowledge about the structure-activity relationship of chemical compounds, the systematic feature selection step in our method offers a convenient means to identify relevant 2D fingerprint-based features. By comparing our method with state-of-the-art linear regression-based methods for the standard Gibbs free energy prediction, we demonstrated that its prediction accuracy and prediction coverage are most favorable. Our results show direct evidence that a number of 2D fingerprints collectively provide useful information about the Gibbs free energy of biochemical reactions and that our systematic feature selection procedure provides a convenient way to identify them. AVAILABILITY AND IMPLEMENTATION: Our software is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Deep learning in bioinformatics: Introduction, application, and perspective in the big data era.

Deep learning, which is especially formidable in handling big data, has achieved great success in various fields, including bioinformatics. With the advances of the big data era in biology, it is foreseeable that deep learning will become increasingly important in the field and will be incorporated in vast majorities of analysis pipelines. In this review, we provide both the exoteric introduction of deep learning, and concrete examples and implementations of its representative applications in bioinformatics. We start from the recent achievements of deep learning in the bioinformatics field, pointing out the problems which are suitable to use deep learning. After that, we introduce deep learning in an easy-to-understand fashion, from shallow neural networks to legendary convolutional neural networks, legendary recurrent neural networks, graph neural networks, generative adversarial networks, variational autoencoder, and the most recent state-of-the-art architectures. After that, we provide eight examples, covering five bioinformatics research directions and all the four kinds of data type, with the implementation written in Tensorflow and Keras. Finally, we discuss the common issues, such as overfitting and interpretability, that users will encounter when adopting deep learning methods and provide corresponding suggestions. The implementations are freely available at https://github.com/lykaust15/Deep_learning_examples.

Inhibitory Effect of the Traditional Chinese Medicine Ephedra sinica granules on Streptococcus pneumoniae Pneumolysin.

Streptococcus pneumoniae (S. pneumoniae) is an opportunistic pathogen that causes pneumonia, meningitis and bacteremia in humans and animals. Pneumolysin (PLY), a major pore-forming toxin that is important for S. pneumoniae pathogenicity, is a promising target for the development of anti-infective agents. Ephedra sinica granules (ESG) is one of the oldest medical preparation with multiple biological activities (such as a divergent wind and cold effect); however, the detailed mechanism remains unknown. In this study, we found that ESG treatment significantly inhibited the oligomerization of PLY and then reduced the activity of PLY without affecting S. pneumoniae growth and PLY production. In a PLY and A549 cell co-incubation system, the addition of ESG resulted in significant protection against PLY-mediated cell injury. Furthermore, S. pneumoniae-infected mice showed decreased mortality, and alleviated tissue damage and inflammatory reactions following treatment with ESG. Our results indicate that ESG is a potential candidate treatment for S. pneumoniae infection that targets PLY. This finding partially elucidates the mechanism of the Chinese herbal formula ESG in the treatment of pneumococcal disease.

YiQi GuBen Formula Inhibits PDGF-BB-Induced Proliferation and Migration of Airway Smooth Muscle Cells.

OBJECTIVE: Increased proliferation and migration of airway smooth muscle cells (ASMCs) are key events in the development of asthma. YiQi GuBen is a traditional Chinese medicinal formula shown to effectively reduce the recurrence rate of asthma and induce anti-asthma effects through multiple pathways; however, its potential role in regulating ASMC proliferation and preventing bronchial asthma remains unexplored. METHODS: This study investigated the effects of YiQi GuBen formula on platelet-derived growth factor (PDGF)-BB-induced ASMC proliferation and migration by methylthiazolyldiphenyl-tetrazolium bromide, wound healing, transwell, and cell cycle assays. The influence of YiQi GuBen formula on nuclear factor-κB (NF-κB) signaling-relevant proteins was measured by Western blotting, real-time quantitative PCR (RT-qPCR) assay, and ELISA. RESULTS: We found that pretreatment with YiQi GuBen formula had a dose-dependent inhibitory effect on PDGF-BB-stimulated ASMC proliferation. It also suppressed PDGF-BB-induced ASMC migration and arrested PDGF-BB-induced cell cycle progression. Furthermore, YiQi GuBen formula suppressed PDGF-BB-induced expression of phosphorylated p65 and the release of inflammatory factors TNF-α, IL-1ß, IL-6, and IL-8 in ASMCs. CONCLUSIONS: In summary, our study shows that YiQi GuBen formula is able to significantly inhibit PDGF-BB-induced ASMC proliferation and migration by suppressing the NF-κB signaling pathway.

Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly.

BACKGROUND: It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years next-generation sequencing technologies have revolutionized the field. The "Read-Split-Walk" (RSW) and "Read-Split-Run" (RSR) methods were developed to identify genome-wide non-canonical spliced regions including special events occurring in cytoplasm. As the significant amount of genome/transcriptome data such as, Encyclopedia of DNA Elements (ENCODE) project, have been generated, we have advanced a newer more memory-efficient version of the algorithm, "Read-Split-Fly" (RSF), which can detect non-canonical spliced regions with higher sensitivity and improved speed. The RSF algorithm also outputs the spliced sequences for further downstream biological function analysis. RESULTS: We used open access ENCODE project RNA-Seq data to search spliced intron sequences against the U12-type spliced intron sequence database to examine whether some events could occur as potential signatures of U12-type splicing. The check was performed by searching spliced sequences against 5'ss and 3'ss sequences from the well-known orthologous U12-type spliceosomal intron database U12DB. Preliminary results of searching 70 ENCODE samples indicated that the presence of 5'ss with U12-type signature is more frequent than U2-type and prevalent in non-canonical junctions reported by RSF. The selected spliced sequences have also been further studied using miRBase to elucidate their functionality. Preliminary results from 70 samples of ENCODE datasets show that several miRNAs are prevalent in studied ENCODE samples. Two of these are associated with many diseases as suggested in the literature. Specifically, hsa-miR-1273 and hsa-miR-548 are associated with many diseases and cancers. CONCLUSIONS: Our RSF pipeline is able to detect many possible junctions (especially those with a high RPKM) with very high overall accuracy and relative high accuracy for novel junctions. We have incorporated useful parameter features into the pipeline such as, handling variable-length read data, and searching spliced sequences for splicing signatures and miRNA events. We suggest RSF, a tool for identifying novel splicing events, is applicable to study a range of diseases across biological systems under different experimental conditions.

Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data.

BACKGROUND: Alternative splicing (AS) is a posttranscriptional process that produces differ-ent transcripts from the same gene and is important to produce diverse protein products in response to environmental stimuli. AS occurs at specific sites on the mRNA sequence, some of which have been de-fined. Multiple bioinformatics tools have been developed to detect AS from experimental data. OBJECTIVES: The goal of this review is to help researchers use specific tools to aid their research and to develop new AS detection tools based on these previously established tools. METHOD: We selected 15 AS detection tools that were recently published; we classified and delineated them on several aspects. Also, a performance comparison of these tools with the same starting input was conducted. RESULT: We reviewed the following categorized features of the tools: Publication information, working principles, generic and distinct workflows, running platform, input data requirement, sequencing depth dependency, reads mapped to multiple locations, isoform annotation basis, precise detected AS types, and performance benchmarks. CONCLUSION: Through comparisons of these tools, we provide a panorama of the advantages and short-comings of each tool and their scopes of application.

Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer.

BACKGROUND: MicroRNAs (miRNA) are short nucleotides that interact with their target genes through 3' untranslated regions (UTRs). The Cancer Genome Atlas (TCGA) harbors an increasing amount of cancer genome data for both tumor and normal samples. However, there are few visualization tools focusing on concurrently displaying important relationships and attributes between miRNAs and mRNAs of both cancer tumor and normal samples. Moreover, a deep investigation of miRNA-mRNA target and biological relationships across multiple cancer types by integrating web-based analysis has not been thoroughly conducted. RESULTS: We developed an interactive visualization tool called MMiRNA-Viewer that can concurrently present the co-relationships of expression between miRNA-mRNA pairs of both tumor and normal samples into a single graph. The input file of MMiRNA-Viewer contains the expression information including fold changes between normal and tumor samples for mRNAs and miRNAs, the correlation between mRNA and miRNA, and the predicted target relationship by a number of databases. Users can also load their own input data into MMiRNA-Viewer and visualize and compare detailed information about cancer-related gene expression changes, and also changes in the expression of transcription-regulating miRNAs. To validate the MMiRNA-Viewer, eight types of TCGA cancer datasets with both normal and control samples were selected in this study and three filter steps were applied subsequently. We performed Gene Ontology (GO) analysis for genes available in final selected 238 pairs and also for genes in the top 5 % (95 percentile) for each of eight cancer types to report a significant number of genes involved in various biological functions and pathways. We also calculated various centrality measurement matrices for the largest connected component(s) in each of eight cancers and reported top genes and miRNAs with high centrality measurements. CONCLUSIONS: With its user-friendly interface, dynamic visualization and advanced queries, we also believe MMiRNA-Viewer offers an intuitive approach for visualizing and elucidating co-relationships between miRNAs and mRNAs of both tumor and normal samples. We suggest that miRNA and mRNA pairs with opposite fold changes of their expression and with inverted correlation values between tumor and normal samples might be most relevant for explaining the decoupling of mRNAs and their targeting miRNAs in tumor samples for certain cancer types.

Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.

BACKGROUND: Most existing tools for detecting next-generation sequencing-based splicing events focus on generic splicing events. Consequently, special types of non-canonical splicing events of short mRNA regions (IRE1α targeted) have not yet been thoroughly addressed at a genome-wide level using bioinformatics approaches in conjunction with next-generation technologies. During endoplasmic reticulum (ER) stress, the gene encoding the RNase Ire1α is known to splice out a short 26 nt region from the mRNA of the transcription factor Xbp1 non-canonically within the cytosol. This causes an open reading frame-shift that induces expression of many downstream genes in reaction to ER stress as part of the unfolded protein response (UPR). We previously published an algorithm termed "Read-Split-Walk" (RSW) to identify non-canonical splicing regions using RNA-Seq data and applied it to ER stress-induced Ire1α heterozygote and knockout mouse embryonic fibroblast cell lines. In this study, we have developed an improved algorithm "Read-Split-Run" (RSR) for detecting genome-wide Ire1α-targeted genes with non-canonical spliced regions at a faster speed. We applied the RSR algorithm using different combinations of several parameters to the previously RSW tested mouse embryonic fibroblast cells (MEF) and the human Encyclopedia of DNA Elements (ENCODE) RNA-Seq data. We also compared the performance of RSR with two other alternative splicing events identification tools (TopHat (Trapnell et al., Bioinformatics 25:1105-1111, 2009) and Alt Event Finder (Zhou et al., BMC Genomics 13:S10, 2012)) utilizing the context of the spliced Xbp1 mRNA as a positive control in the data sets we identified it to be the top cleavage target present in Ire1α (+/-) but absent in Ire1α (-/-) MEF samples and this comparison was also extended to human ENCODE RNA-Seq data. RESULTS: Proof of principle came in our results by the fact that the 26 nt non-conventional splice site in Xbp1 was detected as the top hit by our new RSR algorithm in heterozygote (Het) samples from both Thapsigargin (Tg) and Dithiothreitol (Dtt) treated experiments but absent in the negative control Ire1α knock-out (KO) samples. Applying different combinations of parameters to the mouse MEF RNA-Seq data, we suggest a General Linear Model (GLM) for both Tg and Dtt treated experiments. We also ran RSR for a human ENCODE RNA-Seq dataset and identified 32,597 spliced regions for regular chromosomes. TopHat (Trapnell et al., Bioinformatics 25:1105-1111, 2009) and Alt Event Finder (Zhou et al., BMC Genomics 13:S10, 2012) identified 237,155 spliced junctions and 9,129 exon skipping events (excluding chr14), respectively. Our Read-Split-Run algorithm also outperformed others in the context of ranking Xbp1 gene as the top cleavage target present in Ire1α (+/-) but absent in Ire1α (-/-) MEF samples. The RSR package including source codes is available at http://bioinf1.indstate.edu/RSR and its pipeline source codes are also freely available at https://github.com/xuric/read-split-run for academic use. CONCLUSIONS: Our new RSR algorithm has the capability of processing massive amounts of human ENCODE RNA-Seq data for identifying novel splice junction sites at a genome-wide level in a much more efficient manner when compared to the previous RSW algorithm. Our proposed model can also predict the number of spliced regions under any combinations of parameters. Our pipeline can detect novel spliced sites for other species using RNA-Seq data generated under similar conditions.

TLR agonists polarize interferon responses in conjunction with dendritic cell vaccination in malignant glioma: a randomized phase II Trial.

In this randomized phase II clinical trial, we evaluated the effectiveness of adding the TLR agonists, poly-ICLC or resiquimod, to autologous tumor lysate-pulsed dendritic cell (ATL-DC) vaccination in patients with newly-diagnosed or recurrent WHO Grade III-IV malignant gliomas. The primary endpoints were to assess the most effective combination of vaccine and adjuvant in order to enhance the immune potency, along with safety. The combination of ATL-DC vaccination and TLR agonist was safe and found to enhance systemic immune responses, as indicated by increased interferon gene expression and changes in immune cell activation. Specifically, PD-1 expression increases on CD4+ T-cells, while CD38 and CD39 expression are reduced on CD8+ T cells, alongside an increase in monocytes. Poly-ICLC treatment amplifies the induction of interferon-induced genes in monocytes and T lymphocytes. Patients that exhibit higher interferon response gene expression demonstrate prolonged survival and delayed disease progression. These findings suggest that combining ATL-DC with poly-ICLC can induce a polarized interferon response in circulating monocytes and CD8+ T cells, which may represent an important blood biomarker for immunotherapy in this patient population.Trial Registration: ClinicalTrials.gov Identifier: NCT01204684.

Antigen presentation by clonally diverse CXCR5+ B cells to CD4 and CD8 T cells is associated with durable response to immune checkpoint inhibitors.

Introduction: Increased T cell infiltration and interferon gamma (IFNγ) pathway activation are seen in tumors of melanoma patients who respond to ICI (immune checkpoint inhibitor) or MAPK pathway inhibitor (MAPKi) therapies. Yet, the rate of durable tumor control after ICI is almost twice that of MAPKi, suggesting that additional mechanisms may be present in patients responding to ICI therapy that are beneficial for anti-tumor immunity. Methods: We used transcriptional analysis and clinical outcomes from patients treated with ICI or MAPKi therapies to delineate immune mechanisms driving tumor response. Results: We discovered response to ICI is associated with CXCL13-driven recruitment of CXCR5+ B cells with significantly higher clonal diversity than MAPKi. Our in vitro data indicate that CXCL13 production was increased in human peripheral blood mononuclear cells by anti-PD1, but not MAPKi, treatment. Higher B cell infiltration and B cell receptor (BCR) diversity allows presentation of diverse tumor antigens by B cells, resulting in activation of follicular helper CD4 T cells (Tfh) and tumor reactive CD8 T cells after ICI therapy. Higher BCR diversity and IFNγ pathway score post-ICI are associated with significantly longer patient survival compared to those with either one or none. Conclusions: Response to ICI, but not to MAPKi, depends on the recruitment of CXCR5+ B cells into the tumor microenvironment and their productive tumor antigen presentation to follicular helper and cytotoxic, tumor reactive T cells. Our study highlights the potential of CXCL13 and B cell based strategies to enhance the rate of durable response in melanoma patients treated with ICI.

Dendritic Cell Vaccination in Conjunction with a TLR Agonist Polarizes Interferon Immune Responses in Malignant Glioma Patients.

Autologous tumor lysate-pulsed dendritic cell (ATL-DC) vaccination is a promising immunotherapy for patients with high grade gliomas, but responses have not been demonstrated in all patients. To determine the most effective combination of autologous tumor lysate-pulsed DC vaccination, with or without the adjuvant toll-like receptor (TLR) agonists poly-ICLC or resiquimod, we conducted a Phase 2 clinical trial in 23 patients with newly diagnosed or recurrent WHO Grade III-IV malignant gliomas. We then performed deep, high-dimensional immune profiling of these patients to better understand how TLR agonists may influence the systemic immune responses induced by ATL-DC vaccination. Bulk RNAseq data demonstrated highly significant upregulation of type 1 and type 2 interferon gene expression selectively in patients who received adjuvant a TLR agonist together with ATL-DC. CyTOF analysis of patient peripheral blood mononuclear cells (PBMCs) showed increased expression of PD-1 on CD4+ T-cells, decreases in CD38 and CD39 on CD8+ T cells and elevated proportion of monocytes after ATL-DC + TLR agonist administration. In addition, scRNA-seq demonstrated a higher expression fold change of IFN-induced genes with poly-ICLC treatment in both peripheral blood monocytes and T lymphocytes. Patients who had higher expression of interferon response genes lived significantly longer and had longer time to progression compared to those with lower expression. The results suggest that ATL-DC in conjunction with adjuvant poly-ICLC induces a polarized interferon response in circulating monocytes and specific activation of a CD8+ T cell population, which may represent an important blood biomarker for immunotherapy in this patient population. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01204684.

Immune checkpoint blockade induces distinct alterations in the microenvironments of primary and metastatic brain tumors.

In comparison with responses in recurrent glioblastoma (rGBM), the intracranial response of brain metastases (BrM) to immune checkpoint blockade (ICB) is less well studied. Here, we present an integrated single-cell RNA-Seq (scRNA-Seq) study of 19 ICB-naive and 9 ICB-treated BrM samples from our own and published data sets. We compared them with our previously published scRNA-Seq data from rGBM and found that ICB led to more prominent T cell infiltration into BrM than rGBM. These BrM-infiltrating T cells exhibited a tumor-specific phenotype and displayed greater activated/exhausted features. We also used multiplex immunofluorescence and spatial transcriptomics to reveal that ICB reduced a distinct CD206+ macrophage population in the perivascular space, which may modulate T cell entry into BrM. Furthermore, we identified a subset of progenitor exhausted T cells that correlated with longer overall survival in BrM patients. Our study provides a comprehensive immune cellular landscape of ICB's effect on metastatic brain tumors and offers insights into potential strategies for improving ICB efficacy for brain tumor patients.

The roles of TGF-ß and VEGF pathways in the suppression of antitumor immunity in melanoma and other solid tumors.

Immune checkpoint blockade (ICB) has become well-known in cancer therapy, strengthening the body's antitumor immune response rather than directly targeting cancer cells. Therapies targeting immune inhibitory checkpoints, such as PD-1, PD-L1, and CTLA-4, have resulted in impressive clinical responses across different types of solid tumors. However, as with other types of cancer treatments, ICB-based immunotherapy is hampered by both innate and acquired drug resistance. We previously reported the enrichment of gene signatures associated with wound healing, epithelial-to-mesenchymal, and angiogenesis processes in the tumors of patients with innate resistance to PD-1 checkpoint antibody therapy; we termed these the Innate Anti-PD-1 Resistance Signatures (IPRES). The TGF-ß and VEGFA pathways emerge as the dominant drivers of IPRES-associated processes. Here, we review these pathways' functions, their roles in immunosuppression, and the currently available therapies that target them. We also discuss recent developments in the targeting of TGF-ß using a specific antibody class termed trap antibody. The application of trap antibodies opens the promise of localized targeting of the TGF-ß and VEGFA pathways within the tumor microenvironment. Such specificity may offer an enhanced therapeutic window that enables suppression of the IPRES processes in the tumor microenvironment while sparing the normal homeostatic functions of TGF-ß and VEGFA in healthy tissues.

Luteolin Binds Streptolysin O Toxin and Inhibits Its Hemolytic Effects and Cytotoxicity.

Group A streptococcus (GAS, Streptococcus pyogenes) is a common pathogen that can cause a variety of human diseases. Streptolysin O (SLO) is an exotoxin produced by GAS. It is a pore-forming toxin (PFT) that exhibits high in vivo toxicity. SLO enables GAS to evade phagocytosis and clearance by neutrophils, induces eukaryotic cell lysis, and activates inflammatory bodies. Luteolin is a natural compound that is produced by a wide range of plant species, and recent studies have shown that luteolin can inhibit the growth and alter the morphological of GAS. Here, we reported that luteolin can weaken the cytotoxicity and hemolytic activity of SLO in vitro. Briefly, luteolin bound SLO with high affinity, inhibited its dissolution of erythrocytes, affected its conformational stability and inhibited the formation of oligomers. To further verify the protective effect of luteolin, we used an in vitro SLO-induced human laryngeal carcinoma epithelial type-2 cells (HEp-2) model. Notably, our results showed luteolin protected HEp-2 cells from SLO induced cytotoxicity and changed in cell membrane permeability. In addition, we explored the role of luteolin in protecting mice from GAS-mediated injury using an aerosolized lung delivery model, and our results indicate that luteolin increases murine survival rate following inoculation with a lethal dose of GAS, and that survival was also associated with decreased pathological damage to lung tissue. Our results suggest that luteolin may be a novel drug candidate for the treatment of GAS infection.

Virtual Screening of Cablin Patchouli Herb as a Treatment for Heat Stress: A Study Based on Network Pharmacology, Molecular Docking, and Experimental Verification.

Heat-related diseases have long been known to damage the structure and function of essential macromolecules such as proteins, lipids, and nucleic acids, thereby compromising the integrity of cells and tissues and the physiological functions of the entire organism. Heat stress is the physical discomfort caused by overheating the body and is also the initial manifestation of heat-related diseases. Cablin patchouli herb (CPB) has been used in China for two thousand years and has been used to treat heat stress, but to date, no related mechanistic research is available. In this study, KEGG and PPI networks and the TCMSP and GEO databases were used to explore the components of CPB in relation to heat stress: quercetin, genkwanin, irisolidone, 3,23-dihydroxy-12-oleanen-28-oic acid, and quercetin 7-O-ß-D-glucoside. The targets identified were EGFR, NCOA1, FOS, HIF1A, NFKBIA, and NCOA2; these proteins were verified by molecular docking and experimental verification. In short, our research represents the first report on the use of the traditional Chinese medicine CPB to treat heat stress and thus has pioneering significance.

Gut Microbiota and SCFAs Play Key Roles in QingFei Yin Recipe Anti-Streptococcal Pneumonia Effects.

Emerging evidence has revealed the presence in animals of a bidirectional regulatory "lung-gut axis" that provides resistance to respiratory infections. Clues to the existence of this system stem from observations that respiratory infections are often accompanied by gastrointestinal symptoms, whereby intestinal microbiota appear to play pivotal roles in combating pathogenic infections. Importantly, short-chain fatty acids (SCFAs) produced by the gut microbiota appear to serve as the biological link between host immune defenses and gut flora. Streptococcus pneumoniae (S.pn), the main cause of lower respiratory tract infections, is involved in more than 1.189 million deaths per year. QingFei Yin (QFY) is known for its excellent therapeutic efficacy in combating bacterial lung infections. In this study, effects of S.pn infection on gut homeostasis were assessed using 16S RNA-based microbiota community profiling analysis. In addition, potential mechanisms underlying QFY recipe beneficial therapeutic effects against bacterial pneumonia were explored using S.pn-infected gut microbiota-depleted mice. Results of data analysis indicated that QFY treatment alleviated lung infection-associated pathogenic processes, while also promoting repair of disordered gut flora and counteracting S.pn infection-associated decreases in levels of SCFAs, particularly of acetate and butyrate. Mechanistically, QFY treatment suppressed inflammatory lung injury through inhibition of the host NF-κB-NLRP3 pathway. These results inspired us to identify precise QFY targets and mechanisms underlying QFY anti-inflammatory effects. In addition, we conducted an in-depth evaluation of QFY as a potential treatment for bacterial pneumonia.

Efficacy and safety of Tuina for treatment of pediatric recurrent respiratory tract infections: A protocol for systematic review and meta-analysis.

BACKGROUND: Recurrent respiratory tract infections (RRTIs) are common respiratory ailments in children. RRTIs are often difficult to control and thus generally have a long-term disease course. Children who receive ineffective treatments or those that experience poor treatment outcomes are prone to developing complications such as edema, cough and asthma. Such complications can seriously hinder a child's growth and development, while also adversely affecting the child's physical and mental health. Tuina massage, a traditional Chinese technique that has been practiced in China for >5000 years, has recently been used to treat RRTIs, with good effect. However, no systematic review of research studies focusing on massage as a treatment for RRTIs can be found in the literature to date. The purpose of this study will be to evaluate the efficacy and safety of Tuina massage for the treatment of pediatric patients who experience RRTIs. METHODS: We will search the following databases using electronic methods: the Chinese Biomedical Literature Database (CBM), the China National Knowledge Infrastructure (CNKI), Wanfang Data (WAN FANG), VIP Information (VIP), MEDLINE, PUBMED, EMBASE, and CINAHL. For each database search, the scope will include articles published between the date of database inception to September 2021. Revman5.4 software will be used to conduct this systematic review and meta-analysis. RESULTS: This meta-analysis will confirm whether Tuina massage is of clinical benefit to pediatric patients who experience RRTIs. CONCLUSION: The results of our systematic review and meta-analysis will be used to formulate conclusions as to whether massage therapy is an effective treatment for children suffering from RRTIs. ETHICS AND DISSEMINATION: This systematic review will evaluate the efficacy and safety of tuina in the treatment of recurrent respiratory tract infections. Since all the data included were published, the systematic review did not require ethical approval. INPLASY REGISTRATION NUMBER: INPLASY202190107.