Screening of Sepsis Biomarkers Based on Bioinformatics Data Analysis

Identification of diagnostic candidate genes in COVID-19 patients with sepsis

PURPOSE

Coronavirus Disease 2019 (COVID-19) and sepsis are closely related. This study aims to identify pivotal diagnostic candidate genes in COVID-19 patients with sepsis.

PATIENTS AND METHODS

We obtained a COVID-19 data set and a sepsis data set from the Gene Expression Omnibus (GEO) database. Identification of differentially expressed genes (DEGs) and module genes using the Linear Models for Microarray Data (LIMMA) and weighted gene co-expression network analysis (WGCNA), functional enrichment analysis, protein-protein interaction (PPI) network construction, and machine learning algorithms (least absolute shrinkage and selection operator (LASSO) regression and Random Forest (RF)) were used to identify candidate hub genes for the diagnosis of COVID-19 patients with sepsis. Receiver operating characteristic (ROC) curves were developed to assess the diagnostic value. Finally, the data set GSE28750 was used to verify the core genes and analyze the immune infiltration.

RESULTS

The COVID-19 data set contained 3,438 DEGs， and 595 common genes were screened in sepsis. sepsis DEGs were mainly enriched in immune regulation. The intersection of DEGs for COVID-19 and core genes for sepsis was 329, which were also mainly enriched in the immune system. After developing the PPI network, 17 node genes were filtered and thirteen candidate hub genes were selected for diagnostic value evaluation using machine learning. All thirteen candidate hub genes have diagnostic value, and 8 genes with an Area Under the Curve (AUC) greater than 0.9 were selected as diagnostic genes.

CONCLUSION

Five core genes (CD3D, IL2RB, KLRC, CD5, and HLA-DQA1) associated with immune infiltration were identified to evaluate their diagnostic utility COVID-19 patients with sepsis. This finding contributes to the identification of potential peripheral blood diagnostic candidate genes for COVID-19 patients with sepsis.

Low expression of the CCL5 gene and low serum concentrations of CCL5 in severe invasive group a streptococcal disease

PURPOSE

Our objective was to elucidate host dependent factors of disease severity in invasive group A Streptococcal disease (iGAS) using transcriptome profiling of iGAS cases of varying degrees of severity at different timepoints. To our knowledge there are no previous transcriptome studies in iGAS patients.

METHODS

We recruited iGAS cases from June 2018 to July 2020. Whole blood samples for transcriptome analysis and serum for biomarker analysis were collected at three timepoints representing the acute (A), the convalescent (B) and the post-infection phase (C). Gene expression was compared against clinical traits and disease course. Serum chemokine ligand 5 (CCL5, an inflammatory cytokine) concentration was also measured.

RESULTS

Forty-five patients were enrolled. After disqualifying degraded or impure RNAs we had 34, 31 and 21 subjects at timepoints A, B, and C, respectively. Low expression of the CCL5 gene correlated strongly with severity (death or need for intensive care) at timepoint A (AUC = 0.92), supported by low concentrations of CCL5 in sera.

CONCLUSIONS

Low gene expression levels and low serum concentration of CCL5 in the early stages of an iGAS infection were associated with a more severe disease course. CCL5 might have potential as a predictor of disease severity. Low expression of genes of cytotoxic immunity, especially CCL5, and corresponding low serum concentrations of CCL5 associated with a severe disease course, i.e. death, or need for intensive care, in early phase of invasive group A Streptococcal disease.

Inflammation and Neurodegeneration in Glaucoma: Isolated Eye Disease or a Part of a Systemic Disorder? - Serum Proteomic Analysis

Introduction

Glaucoma is the most common optic neuropathy and the leading cause of irreversible blindness worldwide, which affects 3.54% of the population aged 40-80 years. Despite numerous published studies, some aspects of glaucoma pathogenesis, serum biomarkers, and their potential link with other diseases remain unclear. Recent articles have proposed that autoimmune, oxidative stress and inflammation may be involved in the pathogenesis of glaucoma.

Methods

We investigated the serum expression of 92 inflammatory and neurotrophic factors in glaucoma patients. The study group consisted of 26 glaucoma patients and 192 healthy subjects based on digital fundography.

Results

Patients with glaucoma had significantly lower serum expression of IL-2Rβ, TWEAK, CX3CL1, CD6, CD5, LAP TGF-beta1, LIF-R, TRAIL, NT-3, and CCL23 and significantly higher expression of IL-22Rα1.

Conclusion

Our results indicate that patients with glaucoma tend to have lower levels of neuroprotective proteins and higher levels of neuroinflammatory proteins, similar to those observed in psychiatric, neurodegenerative and autoimmune diseases, indicating a potential link between these conditions and glaucoma pathogenesis.

High-dimensional phenotyping of the peripheral immune response in community-acquired pneumonia

Background

Community-acquired pneumonia (CAP) represents a major health burden worldwide. Dysregulation of the immune response plays an important role in adverse outcomes in patients with CAP.

Methods

We analyzed peripheral blood mononuclear cells by 36-color spectral flow cytometry in adult patients hospitalized for CAP (n=40), matched control subjects (n=31), and patients hospitalized for COVID-19 (n=35).

Results

We identified 86 immune cell metaclusters, 19 of which (22.1%) were differentially abundant in patients with CAP versus matched controls. The most notable differences involved classical monocyte metaclusters, which were more abundant in CAP and displayed phenotypic alterations reminiscent of immunosuppression, increased susceptibility to apoptosis, and enhanced expression of chemokine receptors. Expression profiles on classical monocytes, driven by CCR7 and CXCR5, divided patients with CAP into two clusters with a distinct inflammatory response and disease course. The peripheral immune response in patients with CAP was highly similar to that in patients with COVID-19, but increased CCR7 expression on classical monocytes was only present in CAP.

Conclusion

CAP is associated with profound cellular changes in blood that mainly relate to classical monocytes and largely overlap with the immune response detected in COVID-19.