Evidence from Machine Learning, Diagnostic Hub Genes in Sepsis and Diagnostic Models based on Xgboost Models, Novel Molecular Models for the Diagnosis of Sepsis

BACKGROUND

Systemic multi-organ dysfunction resulting from dysregulated immune responses in the host triggered by microbial infection or other factors is a major cause of death in sepsis, and secretory pathways play an important role in it.

METHODS

GSE57065, GSE65682, GSE145227, and GSE54514 from Gene Expression Omnibus (GEO) were derived for this study. Secretory pathways single sample gene set enrichment analysis (ssGSEA) scores in sepsis and normal samples were exposed. Gene modules associated with secretory pathways were selected by weighted gene coexpression network analysis (WGCNA) for Protein-Protein Interaction Networks (PPI) assessment, and crossover genes in both were evaluated by eXtreme Gradient Boosting (XGBoost) model in feature selection to identify hub genes in sepsis. In addition, we explored the immune cells and signaling pathways regulated by hub genes.

RESULTS

Remarkable dysregulation of secretory pathways was demonstrated in sepsis. The secretory pathways-associated gene modules were intimately involved in cytokine and immune responses in infection. Four crossover genes (CD163, FCER1G, C3AR1, ARG1) were present in WGCNA and PPI, and training in the XGBoost model revealed the best diagnostic performance of these 4 genes, meaning that these genes were the hub genes for sepsis. The 4-hub genes showed a significant negative correlation with T cell activity and a significant positive correlation with inflammatory immune cells. In addition, we found that the 4-hub genes markedly positively regulated INFLAMMATORY RESPONSE, IL6 JAK STAT3 SIGNALING.

CONCLUSION

Based on WGCNA, PPI, and XGBoost models, we identified hub genes that play an important regulatory role in sepsis. We also developed novel molecular models for the diagnosis of sepsis.

Secretory pathways and multiple functions of nonstructural protein 1 in flavivirus infection

The genus Flavivirus contains a wide variety of viruses that cause severe disease in humans, including dengue virus, yellow fever virus, Zika virus, West Nile virus, Japanese encephalitis virus and tick-borne encephalitis virus. Nonstructural protein 1 (NS1) is a glycoprotein that encodes a 352-amino-acid polypeptide and has a molecular weight of 46-55 kDa depending on its glycosylation status. NS1 is highly conserved among multiple flaviviruses and occurs in distinct forms, including a dimeric form within the endoplasmic reticulum, a cell-associated form on the plasma membrane, or a secreted hexameric form (sNS1) trafficked to the extracellular matrix. Intracellular dimeric NS1 interacts with other NSs to participate in viral replication and virion maturation, while extracellular sNS1 plays a critical role in immune evasion, flavivirus pathogenesis and interactions with natural vectors. In this review, we provide an overview of recent research progress on flavivirus NS1, including research on the structural details, the secretory pathways in mammalian and mosquito cells and the multiple functions in viral replication, immune evasion, pathogenesis and interaction with natural hosts, drawing together the previous data to determine the properties of this protein.

Enhanced metabolism and negative regulation of ER stress support higher erythropoietin production in HEK293 cells

Recombinant protein production can cause severe stress on cellular metabolism, resulting in limited titer and product quality. To investigate cellular and metabolic characteristics associated with these limitations, we compare HEK293 clones producing either erythropoietin (EPO) (secretory) or GFP (non-secretory) protein at different rates. Transcriptomic and functional analyses indicate significantly higher metabolism and oxidative phosphorylation in EPO producers compared with parental and GFP cells. In addition, ribosomal genes exhibit specific expression patterns depending on the recombinant protein and the production rate. In a clone displaying a dramatically increased EPO secretion, we detect higher gene expression related to negative regulation of endoplasmic reticulum (ER) stress, including upregulation of ATF6B, which aids EPO production in a subset of clones by overexpression or small interfering RNA (siRNA) knockdown. Our results offer potential target pathways and genes for further development of the secretory power in mammalian cell factories.

The Recruitment of Neutrophils to the Tumor Microenvironment Is Regulated by Multiple Mediators

Neutrophils sense and migrate towards chemotactic factors released at sites of infection/inflammation and contain the affected area using a variety of effector mechanisms. Aside from these established immune defense functions, neutrophils are emerging as one of the key tumor-infiltrating immune cells that influence cancer progression and metastasis. Neutrophil recruitment to the tumor microenvironment (TME) is mediated by multiple mediators including cytokines, chemokines, lipids, and growth factors that are secreted from cancer cells and cancer-associated stromal cells. However, the molecular mechanisms that underlie the expression and secretion of the different mediators from cancer cells and how neutrophils integrate these signals to reach and invade tumors remain unclear. Here, we discuss the possible role of the epithelial to mesenchymal transition (EMT) program, which is a well-established promoter of malignant potential in cancer, in regulating the expression and secretion of these key mediators. We also summarize and review our current understanding of the machineries that potentially control the secretion of the mediators from cancer cells, including the exocytic trafficking pathways, secretory autophagy, and extracellular vesicle-mediated secretion. We further reflect on possible mechanisms by which different mediators collaborate by integrating their signaling network, and particularly focus on TGF-β, a cytokine that is highly expressed in invasive tumors, and CXCR2 ligands, which are crucial neutrophil recruiting chemokines. Finally, we highlight gaps in the field and the need to expand current knowledge of the secretory machineries and cross-talks among mediators to develop novel neutrophil targeting strategies as effective therapeutic options in the treatment of cancer.

Secretion of Nonstructural Protein 1 of Dengue Virus from Infected Mosquito Cells: Facts and Speculations

Dengue virus nonstructural protein 1 (NS1) is a multifunctional glycoprotein. For decades, the notion in the field was that NS1 is secreted exclusively from vertebrate cells and not from mosquito cells. However, recent evidence shows that mosquito cells also secrete NS1 efficiently. In this review, we discuss the evidence for secretion of NS1 of dengue virus, and of other flaviviruses, from mosquito cells, differences between NS1 secreted from mosquito and NS1 secreted from vertebrate cells, and possible roles of soluble NS1 in the insect flavivirus vector.

Plant secretomics: identification, isolation, and biological significance under environmental stress

Plant secretomes are the proteins secreted by the plant cells and are involved in the maintenance of cell wall structure, relationship between host and pathogen, communication between different cells in the plant, etc. Amalgamation of methodologies like bioinformatics, biochemical, and proteomics are used to separate, classify, and outline secretomes by means of harmonizing in planta systems and in vitro suspension cultured cell system (SSCs). We summed up and explained the meaning of secretome, methods used for the identification and isolation of secreted proteins from extracellular space and methods for the assessment of purity of secretome proteins in this review. Two D PAGE method and HPLC based methods for the analysis together with different bioinformatics tools used for the prediction of secretome proteins are also discussed. Biological significance of secretome proteins under different environmental stresses, i.e., salt stress, drought stress, oxidative stress, etc., defense responses and plant interactions with environment are also explained in detail.