Interleukin-6 Signaling Pathway Research Articles

Influence of different sample preparation strategies on hypothesis-driven shotgun proteomic analysis of human saliva

Abstract This research aimed to find an efficient and repeatable bottom-up proteolytic strategy to process the unstimulated human saliva. The focus is on monitoring immune system activation via the cytokine and interleukin signaling pathways. Carbohydrate metabolism is also being studied as a possible trigger of inflammation and joint damage in the context of the diagnostic procedure of temporomandibular joint disorder. The preparation of clean peptide mixtures for liquid chromatography–mass spectrometry analysis was performed considering different aspects of sample preparation: the filter-aided sample preparation (FASP) with different loadings of salivary proteins, the unfractionated saliva, amylase-depleted, and amylase-enriched salivary fractions. To optimize the efficiency of the FASP method, the protocols with the digestion in the presence of 80% acetonitrile and one-step digestion in the presence of 80% acetonitrile were used, omitting protein reduction and alkylation. The digestion procedures were repeated in the standard in-solution mode. Alternatively, the temperature of 24 and 37°C was examined during the trypsin digestion. DyNet analysis of the hierarchical networks of Gene Ontology terms corresponding to each sample preparation method for the bottom-up assay revealed the wide variability in protein properties. The method can easily be tailored to the specific samples and groups of proteins to be examined.

Five immune-related genes as diagnostic markers for endometriosis and their correlation with immune infiltration.

Endometriosis (EMS) is a chronic disease that can cause dysmenorrhea, chronic pelvic pain, and infertility, among other symptoms. EMS diagnosis is often delayed compared to other chronic diseases, and there are currently no accurate, easily accessible, and non-invasive diagnostic tools. Therefore, it is important to elucidate the mechanism of EMS and explore potential biomarkers and diagnostic tools for its accurate diagnosis and treatment. In the present study, we comprehensively analyzed the differential expression, immune infiltration, and interactions of EMS-related genes in three Homo sapiens datasets. Our results identified 332 differentially expressed genes (DEGs) associated with EMS. Gene ontology analysis showed that these changes mainly focused on the positive regulation of endometrial cell proliferation, cell metabolism, and extracellular space, and EMS involved the integrin, complement activation, folic acid metabolism, interleukin, and lipid signaling pathways. The LASSO regression model was established using immune DEGs with an area under the curve of 0.783 for the internal dataset and 0.656 for the external dataset. Five genes with diagnostic value, ACKR1, LMNB1, MFAP4, NMU, and SEMA3C, were screened from M1 and M2 macrophages, activated mast cells, neutrophils, natural killer cells, follicular T helper cells, CD8+, and CD4+ cells. A protein−protein interaction network based on the immune DEGs was constructed, and ten hub genes with the highest scores were identified. Our results may provide a framework for the development of pathological molecular networks in EMS.

In vivo immunomodulation of IL6 signaling in a murine multiple trauma model

A significant number of trauma patients die during the ICU phase of care because of a severe immune response. Interleukin-6 (IL6) plays a central role within that immune response, signaling through a membrane-bound (IL6-R) and a soluble IL6 receptor (sIL6-R). IL6 and the sIL6-R can form an agonistic IL6/sIL6-R-complex, activating numerous cells that are usually not IL6 responsive, a process called trans-signaling. We attempted to demonstrate that modulation of the IL6 signaling (classic signaling and trans-signaling) can attenuate the devastating immune response after trauma in a murine multiple trauma model. Mice were allocated to three study arms: sham, fracture or polytrauma. Half of the animals had the application of an IL6-R antibody following an intervention. After a pre-set time, blood samples were analysed for IL6 and sIL6-R serum levels, organs were analysed for neutrophil infiltration and end organ damage was evaluated. IL6 and sIL6-R showed a rapid peak after fracture, and much more markedly after polytrauma. These parameters were reduced significantly by globally blocking IL6 signaling via IL6-R antibody (Mab) application. Shock organ analysis also illustrated significant neutrophil infiltration following polytrauma, which was also abated via IL6-R Mab application. Furthermore, end organ damage was reduced by IL6-R Mab application. The study results prove the regulatory role of IL6 signaling pathways in polytrauma, with haemorrhagic shock being a major trigger of inflammatory response. Modulation of IL6 signaling shows promise in the prevention of adverse events like organ failure following major trauma and might be a target for in vivo immunomodulation to reduce mortality in severely injured patients, but further evaluation regarding classic IL6 signaling and IL6 trans-signaling is needed.

Integrative bioinformatics analysis to identify the effects of circadian rhythm on Crohn's disease.

Background: Crohn’s disease (CD) is a multifactorial inflammatory bowel disease characterized by complex aberrant autoimmune disorders. Currently, the involvement of the circadian rhythm in the pathogenesis of CD is unknown. Methods: Bulk and single-cell RNA-seq data and associated clinical data from patients with CD were downloaded from the Gene Expression Omnibus (GEO). Single-sample gene set enrichment analysis was performed to calculate the enrichment score (ES) of circadian rhythm-related genes. Differential expression analysis was used to identify differentially expressed genes. Functional enrichment analysis was used to explore potential disease mechanisms. CIBERSORT was used to estimate immune cell abundance. Single-cell RNA-seq data were analyzed using the R package “Seurat.” Results: The ES of circadian rhythm-related genes was lower in the CD tissue than in the normal tissue. Ubiquitin-specific protease 2 (USP2), a circadian rhythm-related gene, was identified as a potential modulator of CD pathogenesis. USP2 expression was reduced in CD and was associated with disease severity. Moreover, the analysis of bulk RNA-seq and single-cell RNA-seq data showed that monocyte and neutrophil abundance was elevated in CD and was negatively correlated with USP2 expression. It should be noted that USP2 expression in acinar cells was negatively correlated with monocyte and neutrophil abundance. Functional enrichment analysis revealed several canonical pathways to be enriched in CD, including the interleukin-17 signaling pathway, tumor necrosis factor signaling pathway, cytokine–cytokine receptor interaction, toll-like receptor signaling pathway, and nod-like receptor signaling pathway. Conclusion: Aberrant expression of circadian rhythm-related genes is correlated with CD pathogenesis. USP2 might be related to crosstalk among the different cell types in CD. These findings provide insights into future chronotherapy for CD.

A real-world study of interleukin-6 receptor blockade in patients with neuromyelitis optica spectrum disorder.

Neuromyelitis optica spectrum disorder (NMOSD) is a relapsing autoimmune disease that can cause permanent neurological disabilities. However, the interleukin-6 (IL-6) signaling pathway is a promising therapeutic target for relapse prevention. Therefore, this study evaluated the long-term effectiveness of tocilizumab, a humanized anti-IL-6 receptor antibody, for NMOSD. We enrolled 65 patients with NMOSD who received regular intravenous administration of tocilizumab (8mg/kg) between October 2017 and January 2022. Then, we retrospectively collected data on the clinical characteristics and baseline glial fibrillary acidic protein (GFAP) and neurofilament light chain levels. The primary outcome was the annualized relapse rate (ARR). Risk factors were assessed using a multivariable logistic regression model. During the median follow-up of 34.1 (interquartile range: 25.5-39.3) months, 23% (15/65) of patients relapsed during tocilizumab treatment, but the median ARR decreased from 1.9 (range 0.12-6.29) to 0.1 (range 0-1.43, p < 0.0001). A prolonged infusion interval (> 4weeks, odds ratio [OR]: 10.7, 95% confidence interval [CI]: 1.6-71.4, p = 0.014) and a baseline plasma GFAP level of > 220pg/mL (OR: 20.6, 95% CI 3.3-129.4, p = 0.001) were risk factors for future relapses. During treatment, the median Expanded Disability Status Scale score significantly decreased in aquaporin-4 antibody-positive and -negative patients, but the pain did not considerably improve. There were no severe safety concerns. Tocilizumab treatment significantly reduced the relapse rate in patients with NMOSD. However, prolonged infusion intervals and high baseline plasma GFAP levels may increase the relapse risk during tocilizumab therapy.

Identification of Potential Prognostic Biomarkers Associated with Monocyte Infiltration in Lung Squamous Cell Carcinoma

The five-year survival rate of lung squamous cell carcinoma is significantly lower than that of other cancer types. It is therefore urgent to discover novel prognosis biomarkers and therapeutic targets and understand their correction with infiltrating immune cells to improve the prognosis of patients with lung squamous cell carcinoma. In this study, we employed robust rank aggregation algorithms to overcome the shortcomings of small sizes and potential bias in each Gene Expression Omnibus dataset of lung squamous cell carcinoma and identified 513 robust differentially expressed genes including 220 upregulated and 293 downregulated genes from six microarray datasets. Functional enrichment analysis showed that these robust differentially expressed genes were obviously involved in the extracellular matrix and structure organization, epidermis development, cell adhesion molecule binding, p53 signaling pathway, and interleukin-17 signaling pathway to affect the progress of lung squamous cell carcinoma. We further identified six hub genes from 513 robust differentially expressed genes by protein-protein interaction network and 10 topological analyses. Moreover, the results of immune cell infiltration analysis from six integrated Gene Expression Omnibus datasets and our sequencing transcriptome data demonstrated that the abundance of monocytes was significantly lower in lung squamous cell carcinoma compared to controls. Immune correlation analysis and survival analysis of hub genes suggested that three hub genes, collagen alpha-1(VII) chain, mesothelin, and chordin-like protein 1, significantly correlated with tumor-infiltrating monocytes as well as may be potential prognostic biomarkers and therapy targets in lung squamous cell carcinoma. The investigation of the correlation of hub gene markers and infiltrating monocytes can also improve to well understand the molecular mechanisms of lung squamous cell carcinoma development.

Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

Due to fast transmission and various circulating SARS-CoV-2 variants, a significant increase of coronavirus 2019 infection cases with acute respiratory symptoms has prompted worries about the efficiency of current vaccines. The possible evasion from vaccine immunity urged scientists to identify novel therapeutic targets for developing improved vaccines to manage worldwide COVID-19 infections. Our study sequenced pooled peripheral blood mononuclear cells transcriptomes of SARS-CoV-2 patients with moderate and critical clinical outcomes to identify novel potential host receptors and biomarkers that can assist in developing new translational nanomedicines and vaccine therapies. The dysregulated signatures were associated with humoral immune responses in moderate and critical patients, including B-cell activation, cell cycle perturbations, plasmablast antibody processing, adaptive immune responses, cytokinesis, and interleukin signaling pathway. The comparative and longitudinal analysis of moderate and critically infected groups elucidated diversity in regulatory pathways and biological processes. Several immunoglobin genes (IGLV9-49, IGHV7-4, IGHV3-64, IGHV1-24, IGKV1D-12, and IGKV2-29), ribosomal proteins (RPL29, RPL4P2, RPL5, and RPL14), inflammatory response related cytokines including Tumor Necrosis Factor (TNF, TNFRSF17, and TNFRSF13B), C-C motif chemokine ligands (CCL3, CCL25, CCL4L2, CCL22, and CCL4), C-X-C motif chemokine ligands (CXCL2, CXCL10, and CXCL11) and genes related to cell cycle process and DNA proliferation (MYBL2, CDC20, KIFC1, and UHCL1) were significantly upregulated among SARS-CoV-2 infected patients. 60S Ribosomal protein L29 (RPL29) was a highly expressed gene among all COVID-19 infected groups. Our study suggested that identifying differentially expressed genes (DEGs) based on disease severity and onset can be a powerful approach for identifying potential therapeutic targets to develop effective drug delivery systems against SARS-CoV-2 infections. As a result, potential therapeutic targets, such as the RPL29 protein, can be tested in vivo and in vitro to develop future mRNA-based translational nanomedicines and therapies to combat SARS-CoV-2 infections.

Molecular mechanisms of Biyu decoction as treatment for psoriasis: A network pharmacology and molecular docking study

BACKGROUNDThe therapeutic effects of a combination of Chinese medicines called Biyu decoction have been clinically verified, although its molecular targets in psoriasis remain unknown. AIMTo explore the molecular mechanisms of Biyu decoction for psoriasis treatment.METHODSIn this network pharmacology and molecular docking study, the Traditional Chinese Medicine Systems Pharmacology database was searched for Biyu decoction active ingredients. GeneCards, Online Mendelian Inheritance in Man, PharmGkb, Therapeutic Target Database, and DrugBank databases were searched for psoriasis-related genes. The genes targeted by the decoction’s active ingredient and disease genes were intersected to obtain predictive targets of the drug during psoriasis treatment. Cytoscape 3.8.0 was used to construct a drug component/ target disease network. The The functional protein association networks database and Cytoscape were used to construct a protein-protein interaction network and streamline the core network. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used for pathway enrichment analysis. Molecular docking technology was used to verify the drug component/target disease network. RESULTSWe screened 117 major active ingredients, including quercetin, kaempferol, naringenin, and acetyl-shikonin, and identified 213 gene targets, such as MAPK3, JUN, FOS, MYC, MAPK8, STAT3, and NFKBIA. Using a molecular docking analysis, the main active ingredients demonstrated good binding to the core targets. The Gene Ontology analysis showed that these ingredients were significantly associated with biological activities, such as transcription factor DNA binding, RNA polymerase II-specific DNA binding of transcription factors, and cytokine receptor binding; responses to lipopolysaccharides, molecules of bacterial origin, and oxidative stress; and were mainly distributed in membrane rafts, microdomains, and regions. The Kyoto Encyclopedia of Genes and Genomes analysis showed that decoction ingredients act on Th17 cell differentiation, tumor necrosis factor and mitogen-activated protein signaling pathways, the interleukin-17 signaling pathway, and the PI3K-Akt signaling pathway. CONCLUSIONBiyu decoction may be effective against psoriasis through multi-component, multi-target, and multi-channel synergy.

The mechanism of action of the combination of Astragalus membranaceus and Ligusticum chuanxiong in the treatment of ischemic stroke based on network pharmacology and molecular docking.

Since 1990, the incidence of stroke has been rising to become the second leading cause of death in the world, posing a huge burden and challenge to society and families. Astragalus membranaceus and Ligusticum chuanxiong (A&L) have been used as traditional Chinese medicine (TCM) prescriptions to treat and prevent the occurrence of ischemic stroke (IS), but their mechanism of action on the disease has not been fully elucidated. The main objective of this study was to reveal the pharmacological mechanism of A&L in the treatment of IS and to perform preliminary validation. The active ingredients of A&L were obtained from the systematic pharmacology platform of traditional Chinese medicine (TCMSP) database, whereas the genes of IS were obtained from 2 major databases, DrugBank and GeneCards. Cytoscape_v3.8.2 was used to construct the TCM-active ingredient and TCM-active ingredient-cross-target-disease relationship maps, and the MCODE plug-in was used to obtain the core genes, whereas the protein-protein interaction maps were obtained from the STRING database. The results of gene ontology and Kyoto encyclopedia of genes and genomes enrichment were obtained using the Hiplot online tool, and the small molecules in the relevant signalling pathways were verified by molecular docking using AutoDock. A&L contained a total of 26 eligible active ingredients, sharing 161 common targets with IS. A total of 58 core genes with 1326 edges were obtained using the MCODE plug-in. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment results showed association with interleukin-17 signaling pathway, lipid and atherosclerosis, tumor necrosis factor signaling pathway, and Toll-like receptor signaling pathway, which mainly mediates the development of inflammatory responses. Furthermore, molecular docking was conducted and most of the components were found to have good binding to the receptors. This study demonstrates that A&L can be used to treat IS by controlling the inflammatory response through multiple targets and multiple pathways, and provides a reference for subsequent trials.

Raft platforms highly enriched in cholesterol: major scaffolds for IL-6 signalling assembly with implications in inflammation and cancer.

Interleukin-6 (IL-6) is a pleiotropic cytokine with complex and major roles in inflammation, which could be linked to the different ways IL-6 signals at the plasma membrane. In this issue of FEBS Journal, Woo and co-workers present evidence for the involvement of Eps15 homology domain-containing protein 1 (EHD1)-mediated lipid raft platforms, highly enriched in cholesterol, in the IL-6 signalling pathway. Because of the strong connection between IL-6, inflammation and cancer, one implication of this report is that agents or approaches targeting cholesterol-rich raft platforms may assist the development of novel strategies to treat inflammatory and malignant diseases. Comment on: https://doi.org/10.1111/febs.16458.

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 10 hub genes in the PPI network were prostaglandin-endoperoxide synthase 2 (Ptgs2), chemokine (C-X-C motif) ligand 2 (Cxcl2), colony-stimulating factor 2 (granulocyte-macrophage) (Csf2), matrix metallopeptidase 13 (Mmp13), amphiregulin (Areg), plasminogen activator, urokinase receptor (Plaur), fos-like antigen 1 (Fosl1), epiregulin (Ereg), activating transcription factor 3 (Atf3), and transferrin receptor (Tfrc). Cxcl2, Csf2, and Atf3 played important roles in the mitogen-activated protein kinase (MAPK) signaling pathway. Conclusions: These pathways and DEGs may serve as targets for gene therapy.

Modeling Kaempferol as a Potential Pharmacological Agent for COVID-19/PF Co-Occurrence Based on Bioinformatics and System Pharmacological Tools

Objective: People suffering from coronavirus disease 2019 (COVID-19) are prone to develop pulmonary fibrosis (PF), but there is currently no definitive treatment for COVID-19/PF co-occurrence. Kaempferol with promising antiviral and anti-fibrotic effects is expected to become a potential treatment for COVID-19 and PF comorbidities. Therefore, this study explored the targets and molecular mechanisms of kaempferol against COVID-19/PF co-occurrence by bioinformatics and network pharmacology. Methods: Various open-source databases and Venn Diagram tool were applied to confirm the targets of kaempferol against COVID-19/PF co-occurrence. Protein-protein interaction (PPI), MCODE, key transcription factors, tissue-specific enrichment, molecular docking, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to clarify the influential molecular mechanisms of kaempferol against COVID-19 and PF comorbidities. Results: 290 targets and 203 transcription factors of kaempferol against COVID-19/PF co-occurrence were captured. Epidermal growth factor receptor (EGFR), proto-oncogene tyrosine-protein kinase SRC (SRC), mitogen-activated protein kinase 3 (MAPK3), mitogen-activated protein kinase 1 (MAPK1), mitogen-activated protein kinase 8 (MAPK8), RAC-alpha serine/threonine-protein kinase (AKT1), transcription factor p65 (RELA) and phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (PIK3CA) were identified as the most critical targets, and kaempferol showed effective binding activities with the above critical eight targets. Further, anti-COVID-19/PF co-occurrence effects of kaempferol were associated with the regulation of inflammation, oxidative stress, immunity, virus infection, cell growth process and metabolism. EGFR, interleukin 17 (IL-17), tumor necrosis factor (TNF), hypoxia inducible factor 1 (HIF-1), phosphoinositide 3-kinase/AKT serine/threonine kinase (PI3K/AKT) and Toll-like receptor signaling pathways were identified as the key anti-COVID-19/PF co-occurrence pathways. Conclusion: Kaempferol is a candidate treatment for COVID-19/PF co-occurrence. The underlying mechanisms may be related to the regulation of critical targets (EGFR, SRC, MAPK3, MAPK1, MAPK8, AKT1, RELA, PIK3CA and so on) and EGFR, IL-17, TNF, HIF-1, PI3K/AKT and Toll-like receptor signaling pathways. This study contributes to guiding development of new drugs for COVID-19 and PF comorbidities.

Biomarker analysis of first-line sintilimab plus gemcitabine and cisplatin in patients with advanced biliary tract cancers: Results from a phase II study.

e16189 Background: The overall efficacy of immunotherapy for advanced biliary tract cancers (BTCs) was still poor, exploring the potential biomarkers associated with tumor response in advanced BTCs may further improve the clinical benefits from immunotherapy. Methods: Twelve patients from a phase 2 clinical trial (ChiCTR2000036652), which evaluated the efficacy and safety of sintilimab (anti-PD-1 antibody), plus gemcitabine and cisplatin as first-line treatment in advanced BTC patients, were included in the current biomarkers analysis. Exploratory points mainly focused on differentiated immune-related gene expression and immune pathway signatures using a 289-gene immune-related RNA panel sequencing on baseline tumor samples. Differential gene expression analysis was performed between responders (tumor regression) and non-responders (tumor extension) using Wilcoxon rank-sum test. Signature scores were calculated using the Gene Set Variation Analysis package with publicly available gene signatures. Results: Twelve patients (8 responders vs. 4 non-responders) who had available clinical response evaluations with RNA-sequencing data on baseline tumor samples were included in the current biomarkers analysis. Differential gene expression analysis revealed a significantly increased CXCL10, CXCL13 expression (p &lt; 0.001) and decreased MAGEA12 expression (p &lt; 0.001) in responder tumors compared with non-responder tumors. Differentiated genes were significantly enriched in cytokine-cytokine receptor interaction and interleukin-17 signaling pathway in responder tumors. Extensive analyses on immune pathway signatures showed that higher expression of IFN-γ-related genes (p = 0.048) and T cell-inflamed genes (p = 0.016) were associated with response to immunocombination therapy. Meanwhile, immune cell types score was also calculated, no notable differences were found between defined groups. Conclusions: Some differentially expressed genes were investigated in responder tumors compared with non-responder tumors. Higher expression of IFN-γ-related genes and T cell-inflamed genes could potentially predict the effect of immunocombination therapy. Potential biomarkers are needed to identify patients who respond to sintilimab plus gemcitabine and cisplatin in a larger validation cohort. Clinical trial information: ChiCTR2000036652.

Transcriptome sequencing analysis revealed the molecular mechanism of podoplanin neutralization inhibiting ischemia/reperfusion-induced microglial activation.

BackgroundAnti-podoplanin antibody (α-PDPN, clone 8.1.1) reduces microglia-mediated inflammation and decreases cerebral infarct volume in mice with stroke. However, the molecular mechanism by which this occurs is unknown. This study sought to systematically analyze the molecular mechanism of α-PDPN treatment on ischemia/reperfusion (I/R)-injured microglia.MethodsMicroglia BV2 cells were pre-cultured with α-PDPN and then exposed to oxygen-glucose deprivation and reoxygenation (OGD-R) insult. The differentially expressed genes (DEGs) underwent a transcriptome sequencing technology analysis, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Quantitative real-time polymerase chain reaction (PCR) was performed to confirm the transcriptional expression of some DEGs.ResultsThe results showed that α-PDPN downregulated 338 genes and upregulated 340 genes in the BV2 cells. The GO items of the downregulated DEGs mainly involved biological processes, such as the response to the interferon (IFN), lipopolysaccharide-mediated signaling pathway, and the regulation of cell chemotaxis and migration. The upregulated molecular function mainly involved glucocorticoid-receptor binding. Further, the KEGG pathway analysis indicated that the enriched categories for the upregulated DEGs mainly involved the adenosine triphosphate (ATP) binding cassette transporters. However, the interleukin-17 signaling pathway, IFN signaling pathway, tumor necrosis factor signaling pathway, transforming growth factor beta (TGF-ꞵ) signaling pathway, nucleotide-binding and oligomerization domain (NOD)-like receptor signaling pathway, cytokine-cytokine receptor interaction, and chemokine signaling pathway were downregulated by the α-PDPN treatment.ConclusionsNumerous inflammation-related signaling pathways were regulated by the α-PDPN treatment in the OGD-R injured BV2 cells. This study provided further insights into the protective mechanism of α-PDPN treatment in ischemic stroke.

Bioinformatics prediction of potential mechanisms and biomarkers underlying dilated cardiomyopathy.

BACKGROUNDHeart failure is a health burden responsible for high morbidity and mortality worldwide, and dilated cardiomyopathy (DCM) is one of the most common causes of heart failure. DCM is a disease of the heart muscle and is characterized by enlargement and dilation of at least one ventricle alongside impaired contractility with left ventricular ejection fraction < 40%. It is also associated with abnormalities in cytoskeletal proteins, mitochondrial ATP transporter, microvasculature, and fibrosis. However, the pathogenesis and potential biomarkers of DCM remain to be investigated.AIMTo investigate the candidate genes and pathways involved in DCM patients.METHODSTwo expression datasets (GSE3585 and GSE5406) were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) between the DCM patients and healthy individuals were identified using the R package “linear models for microarray data.” The pathways with common DEGs were analyzed via Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analyses. Moreover, a protein-protein interaction network (PPI) was constructed to identify the hub genes and modules. The MicroRNA Database was applied to predict the microRNAs (miRNAs) targeting the hub genes. Additionally, immune cell infiltration in DCM was analyzed using CIBERSORT.RESULTSIn total, 97 DEGs (47 upregulated and 50 downregulated) were identified. GO analysis showed that the DEGs were mainly enriched in “response to growth factor,” “extracellular matrix,” and “extracellular matrix structural constituent.” KEGG pathway analysis indicated that the DEGs were mainly enriched in “protein digestion and absorption” and “interleukin 17 (IL-17) signaling pathway.” The PPI network suggested that collagen type III alpha 1 chain (COL3A1) and COL1A2 contribute to the pathogenesis of DCM. Additionally, visualization of the interactions between miRNAs and the hub genes revealed that hsa-miR-5682 and hsa-miR-4500 interacted with both COL3A1 and COL1A2, and thus these miRNAs might play roles in DCM. Immune cell infiltration analysis revealed that DCM patients had more infiltrated plasma cells and fewer infiltrated B memory cells, T follicular helper cells, and resting dendritic cells.CONCLUSIONCOL1A2 and COL3A1 and their targeting miRNAs, hsa-miR-5682 and hsa-miR-4500, may play critical roles in the pathogenesis of DCM, which are closely related to the IL-17 signaling pathway and acute inflammatory response. These results may provide useful clues for the diagnosis and treatment of DCM.

Diagnosis and Prediction of Endometrial Carcinoma Using Machine Learning and Artificial Neural Networks Based on Public Databases.

Endometrial carcinoma (EC), a common female reproductive system malignant tumor, affects thousands of people with high morbidity and mortality worldwide. This study was aimed at developing a prediction model for the diagnosis of EC in the general population. First, we obtained datasets GSE63678, GSE106191, and GSE115810 from the Gene Expression Omnibus (GEO) database, dataset GSE17025 from the GEO database, and the RNA sequence of EC from The Cancer Genome Atlas (TCGA) database to constitute the training, test, and validation groups, respectively. Subsequently, the 96 most significantly differentially expressed genes (DEGs) were identified and analyzed for function and pathway enrichment in the training group. Next, we acquired the disease-specific genes by random forest and established an artificial neural network for the diagnosis. Receiver operating characteristic (ROC) curves were utilized to identify the signature across the three groups. Finally, immune infiltration was analyzed to reveal tumor-immune microenvironment (TIME) alterations in EC. The top 96 DEGs (77 down-regulated and 19 up-regulated genes) were primarily enriched in the interleukin-17 signaling pathway, protein digestion and absorption, and transcriptional misregulation in cancer. Subsequently, 14 characterizing genes of EC were identified by random forest. In the training, test, and validation groups, the artificial neural network was constructed with high diagnostic accuracies of 0.882, 0.864, and 0.839, respectively, and areas under the ROC curve (AUCs) of 0.928, 0.921, and 0.782, respectively. Finally, resting and activated mast cells were found to have increased in TIME. We constructed an artificial diagnostic model with excellent reliability for EC and uncovered variations in the immunological ecosystem of EC through integrated bioinformatics approaches, which might be potential diagnostic targets for EC.

Interleukin-6 Signaling in Triple Negative Breast Cancer Cells Elicits the Annexin A1/Formyl Peptide Receptor 1 Axis and Affects the Tumor Microenvironment.

Annexin A1 (AnxA1) is a pleiotropic protein that exerts essential roles in breast cancer (BC) growth and aggressiveness. In our previous work, we described the autocrine signaling of AnxA1 through formyl peptide receptor 1 (FPR1) in the triple-negative (TN) BC cell line, MDA-MB-231. Here, we aimed to describe the interaction between the AnxA1/FPR1 and the Interleukin-6 (IL-6) signaling pathways and their role in the tumor microenvironment (TME). First, we demonstrated that AnxA1 and IL-6 expression levels are correlated in BC tissue samples. In three TNBC cell lines, overexpression of both AnxA1 and IL-6 was also identified. Next, we inhibited FPR1, the IL-6 receptor and STAT3 in both MDA-MB-231 and MDA-MB-157 cells. The FPR1 inhibition led to increased levels of IL-6 and secreted AnxA1 in both cell lines. On the other side, inhibition of the IL-6 receptor or STAT3 led to the impairment of AnxA1 secretion, suggesting the essential role of the IL-6 signaling cascade in the activation of the AnxA1/FPR1 autocrine axis. Finally, we described the interaction between IL-6 and the AnxA1/FPR1 pathways and their role on the TME by analyzing the effect of supernatants derived from MDA-MB-231 and MDA-MB-157 cells under the inhibition of FPR1 or IL-6 signaling on fibroblast cell motility.

Radiation Exposure Perturbs IL-17RA-Mediated Immunity Leading to Changes in Neutrophil Responses That Increase Susceptibility to Oropharyngeal Candidiasis.

Fungal infections caused by Candida albicans are a serious problem for immunocompromised individuals, including those undergoing radiotherapy for head and neck cancers. Targeted irradiation causes inflammatory dysregulation and damage to the oral mucosa that can be exacerbated by candidiasis. Post-irradiation the cytokine interleukin-17 (IL-17) protects the oral mucosae by promoting oral epithelial regeneration and balancing the oral immune cell populations, which leads to the eventual healing of the tissue. IL-17 signaling is also critical for the antifungal response during oropharyngeal candidiasis (OPC). Yet, the benefit of IL-17 during other forms of candidiasis, such as vulvovaginal candidiasis, is not straightforward. Therefore, it was important to determine the role of IL-17 during OPC associated with radiation-induced inflammatory damage. To answer this question, we exposed Il17ra−/− and wild-type mice to head-neck irradiation (HNI) and OPC to determine if the IL-17 signaling pathway was still protective against C. albicans. HNI increased susceptibility to OPC, and in Il17ra−/− mice, the mucosal damage and fungal burden were elevated compared to control mice. Intriguingly, neutrophil influx was increased in Il17ra−/− mice, yet these cells had reduced capacity to phagocytose C. albicans and failed to clear OPC compared to immunocompetent mice. These findings suggest that radiotherapy not only causes physical damage to the oral cavity but also skews immune mediators, leading to increased susceptibility to oropharyngeal candidiasis.

Meprin β Modulates Cellular Proliferation Through The IL‐6 Signaling Pathway In IRInduced Kidney Injury

Inflammation plays a central role in the progression of kidney injury induced by ischemia/reperfusion (IR). Interleukin‐6 (IL‐6) trans‐signaling has been shown to play a protective role by promoting repair processes in IR‐induced renal injury. Meprin metalloproteases have been implicated in inflammation‐induced kidney injury. Meprins proteolytically process the proinflammatory cytokine, IL‐6, causing IL‐6 inactivation. It was recently reported that meprins also cleave the IL‐6 receptor (IL‐6R). IL‐6 binds to its receptor (IL‐6R) in two ways, membrane bound (mbIL‐6R), activating the classic IL‐6 signaling pathway, or the soluble form (sIL‐6R), activating the IL‐6 trans‐signaling pathway. IL‐6 trans‐signaling induces proliferation through either MAPK/ERK or PI3K/AKT pathway or in crosstalk with AKT/ERK. We previously showed that meprin β modulates cellular survival (BCL‐2) through IL‐6/JAK/STAT signaling pathway in IRinduced kidney injury. However, it’s not known how meprin β modulation of the IL‐6 signaling pathway impacts the cellular proliferation in IR‐induced acute kidney injury. Previous studies have shown that IL‐6 binds to its receptor forming IL‐6/IL6R complex, which binds to the membranebound gp130 dimer. This leads to activation phosphorylation of ERK and AKT pathways, which in turn leads to induction of cellular proliferation. PCNA is a cellular proliferation marker that is induced through activation of the IL‐6 signaling pathway. The goal of the current study was to determine how meprin β modulation of the IL‐6 signaling pathway impacts downstream cellular proliferation in IR‐induced kidney injury. We used the unilateral IR as a model of renal inflammation in wild‐type (WT) and meprin β knockout (βKO) male mice, with the contralateral kidneys serving as controls. The mice were sacrificed at 96 h post‐IR, and kidney tissue processed for evaluation by RT‐PCR and immunohistochemistry (IHC). To determine staining intensity, the tissue sections were evaluated for IL‐6 and PCNA levels using light microscopy and imaged using Image J analysis Software. Statistical analysis of the optical density (OD) data utilized two‐way ANOVA. Our PCR data showed a significant increase in mRNA levels for IL‐6 and PCNA in WT and βKO mice (P ≤ 0.01) at 96 h‐post IR when compared to WT control kidneys. However, the baseline mRNA levels for PCNA were significantly higher in βKO (P ≤ 0.01) when compared to WT kidneys. Immunohistochemical data showed significant increases (P&lt;0.05) in IL‐6 and PCNA in select tubules in both genotypes at 96 h post‐IR when compared to control kidneys for each genotype. Data from immunofluorescence counterstaining of kidney tissues showed that the levels of IL‐6, and PCNA were higher in meprin β‐expressing proximal tubules (PTs), at 96 h post‐IR when compared to the distal kidney tubules (DTs), which lack meprins. High levels of IL‐6 were also present in the lumen of PTs and DTs from WT and βKO kidneys at 96 h post‐IR, suggesting increased release into filtrate and subsequently into urine. However, high levels of PCNA were present in the lumen of PTs only from both genotypes at 96 h post‐IR. In conclusion, our data shows that meprin β expression modulates cellular proliferation through the IL‐6 signaling pathway in IR‐induced kidney injury.

Immune-Related Biomarkers Associated with Lung Metastasis from the Colorectal Cancer Microenvironment.

Immune-associated biomarkers can predict lung metastases from colorectal cancer. Differentially expressed genes (DEGs) were screened from sample data extracted from gene expression omnibus (GEO) database. The DEGs were screened from the lung metastasis (LM) and primary cancer (PC) groups of the Moffitt Cancer Center cohort dataset. Then, the tumor immune microenvironment and abundance of immune cell infiltration analyses were performed, and the immune-related DEGs were retrieved. In addition, the transcription factor (TF)-miRNA-mRNA network was constructed and enrichment analyses of the immune-related DEGs and upregulated and downregulated DEGs were carried out. Then, the protein-protein interaction (PPI) network was conducted and the drug-gene interaction was predicted. A total of 268 DEGs were screened. The Immune_Score of samples in the LM group was significantly higher compared with the PC group. The infiltration ratio of M0 macrophages and M2 macrophages of samples was higher than others. A total of 54 immune-related DEGs in M0 macrophages were screened. Moreover, the TF-miRNA-mRNA network was constructed among 8 miRNA-mRNA and 50 TF-mRNA, and the secreted phosphoprotein 1 was regulated by 12 TFs, and the oxidized low-density lipoprotein receptor 1 was regulated by 3 miRNAs and 3 TFs. The TF SAM pointed domain containing ETS TF was also a downregulated DEG. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the DEGs in the TF-miRNA-mRNA network were mainly involved in the interleukin-7 signaling pathway and cell adhesion molecules. In total, 23 protein interactions in this PPI network of M0 macrophage cells were involved in 27 mRNAs. There were 38 drug-gene interactions of immune-related DEGs of M0 macrophage cells predicted to contain 34 small molecule drugs and 8 mRNAs. Finally, the CON cohort dataset verified that the infiltration ratio of M0 and M2 macrophages of the samples was higher.