Co-expression and interaction network analysis reveals dysregulated neutrophil and T-cell activation as the core mechanism associated with septic shock

Identification of key genes as potential diagnostic biomarkers in sepsis by bioinformatics analysis

Background

Sepsis, an infection-triggered inflammatory syndrome, poses a global clinical challenge with limited therapeutic options. Our study is designed to identify potential diagnostic biomarkers of sepsis onset in critically ill patients by bioinformatics analysis.

Methods

Gene expression profiles of GSE28750 and GSE74224 were obtained from the Gene Expression Omnibus (GEO) database. These datasets were merged, normalized and de-batched. Weighted gene co-expression network analysis (WGCNA) was performed and the gene modules most associated with sepsis were identified as key modules. Functional enrichment analysis of the key module genes was then conducted. Moreover, differentially expressed gene (DEG) analysis was conducted by the "limma" R package. Protein-protein interaction (PPI) network was created using STRING and Cytoscape, and PPI hub genes were identified with the cytoHubba plugin. The PPI hub genes overlapping with the genes in key modules of WGCNA were determined to be the sepsis-related key genes. Subsequently, the key overlapping genes were validated in an external independent dataset and sepsis patients recruited in our hospital. In addition, CIBERSORT analysis evaluated immune cell infiltration and its correlation with key genes.

Results

By WGCNA, the greenyellow module showed the highest positive correlation with sepsis (0.7, p = 2e - 19). 293 DEGs were identified in the merged datasets. The PPI network was created, and the CytoHubba was used to calculate the top 20 genes based on four algorithms (Degree, EPC, MCC, and MNC). Ultimately, LTF, LCN2, ELANE, MPO and CEACAM8 were identified as key overlapping genes as they appeared in the PPI hub genes and the key module genes of WGCNA. These sepsis-related key genes were validated in an independent external dataset (GSE131761) and sepsis patients recruited in our hospital. Additionally, the immune infiltration profiles differed significantly between sepsis and non-sepsis critical illness groups. Correlations between immune cells and these five key genes were assessed, revealing that plasma cells, macrophages M0, monocytes, T cells regulatory, eosinophils and NK cells resting were simultaneously and significantly associated with more than two key genes.

Conclusion

This study suggests a critical role of LTF, LCN2, ELANE, MPO and CEACAM8 in sepsis and may provide potential diagnostic biomarkers and therapeutic targets for the treatment of sepsis.

Botulinum toxin type A ameliorates rat dorsal root ganglia neuron pyroptosis in postherpetic neuralgia by upregulating cathelicidin antimicrobial peptide to inhibit neutrophil elastase

Botulinum toxin type A (BoNT/A) has exhibited efficacy in postherpetic neuralgia (PHN) treatment, and this study aims to uncover its underlying mechanisms. Resiniferatoxin (RTX)-induced PHN rats were given BoNT/A. Rat postoperative pain behaviors were assessed by Von Frey test. Cleaved-synaptosomal protein 25 kDa (cl-SNAP-25) or cathelicidin antimicrobial peptide (CAMP) expression in rat dorsal root ganglia (DRG) was detected by immunofluorescence or immunohistochemistry. Healthy rat-derived DRG neurons were transfected, incubated with lipopolysaccharides (LPS)/adenosine 5'-triphosphate (ATP) to stimulate pyroptosis and treated with BoNT/A. The CCK-8, Western blot, ELISA, and qRT-PCR were used to assess the viability, levels of pyroptosis-related proteins proinflammatory cytokine levels, as well as CAMP and ELANE mRNA levels. BoNT/A (30 U/kg) promoted cl-SNAP-25 expression in rat DRG and reversed RTX-induced decrease of rat paw withdrawal thresholds and CAMP expression and increase of pyroptosis-associated protein and inflammatory factor expression in rat DRG. CAMP interacted with ELANE in rat DRG neurons. BoNT/A attenuated LPS/ATP-stimulated inhibition of viability and CAMP expression and upregulation of inflammatory mediators, pyroptosis-related proteins, and ELANE expression in rat DRG neurons, which was counteracted by CAMP silencing. However, ELANE knockdown offset the effect of CAMP silencing in LPS/ATP/BoNT/A-treated rat DRG neurons. On the whole, BoNT/A alleviates rat DRG neuron pyroptosis during PHN by upregulating CAMP to inhibit ELANE.

Comparative analysis of peripheral blood immunoinflammatory landscapes in patients with acute cholangitis and its secondary septic shock using single-cell RNA sequencing

BACKGROUND

Acute cholangitis (AC) is a key pathogeny of septic shock, which has a high mortality rate. AC has significant clinical heterogeneity, but no study has analyzed the discrepancies in immunoresponsiveness between AC and its secondary septic shock. The immune inflammatory responses play a critical role in the development of septic shock.

METHODS

We performed single-cell RNA sequencing (scRNA-seq) to analyze the differences of immunocytes in immunoresponse and inflammation between the early stages of AC (A1, A2, and A3) and its secondary septic shock (B1, B2, and B3).

RESULTS

This study has identified seven cell types, including T cells, B cells, plasma cells, neutrophils, monocytes, platelets and erythrocytes. We mainly focused on neutrophils, monocytes, and T cells. Neutrophil subpopulation analysis indicated that neutrophil progenitors (proNeus) were identified in neutrophil subsets. Compared with patients suffering from AC, the gene phenotypes of proNeus (ELANE, AZU1, MPO, and PRTN3) were significantly upregulated in septic shock. The differentiation direction of neutrophil subsets in peripheral blood mononuclear cells (PBMCs) was determined; Moreover, the proNeus in septic shock presented a state of "expansion", with upregulation of neutrophil degranulation and downregulation of monocyte and T cell proliferation. Neutrophils-7 (CCL5, RPL23A, RPL13, RPS19 and RPS18) were mainly involved in the regulation of cellular functions. The neutrophils-7 subpopulation in septic shock were in a state of "exhaustion", and its biological functions showed the characteristics of weakening neutrophil migration and phagocytosis, etc., which maked infection difficult to control and aggravated the development of septic shock. Analysis of monocyte and T cell subpopulations showed that the expression genes and biological functions of subpopulations were closely related to immunoinflammatory regulation. In addition, CCL3 - CCR1, CXCL1 - CXCR2 and other ligand-receptors were highly expressed in neutrophils and monocytes, enhancing interactions between immune cells.

CONCLUSION

ScRNA-seq revealed significant differences in immune cells between AC and its secondary septic shock, which were primarily manifested in the cellular numbers, differentially expressed genes, functions of cellular subsets, differentiation trajectories, cell-cell interactions and so on. We identified many subsets of neutrophil, T cell and monocyte were associated with inflammation and immunosuppression induced by septic shock. These provided a reference for accurately evaluating the pathological severity of patients with AC and discovering the targets for therapy.