Identification of Nine mRNA Signatures for Sepsis Using Random Forest

Prediction of sepsis among patients with major trauma using artificial intelligence: a multicenter validated cohort study

BACKGROUND

Sepsis remains a significant challenge in patients with major trauma in the ICU. Early detection and treatment are crucial for improving outcomes and reducing mortality rates. Nonetheless, clinical tools for predicting sepsis among patients with major trauma are limited. This study aimed to develop and validate an artificial intelligence (AI) platform for predicting the risk of sepsis among patients with major trauma.

PATIENTS AND METHODS

This study involved 961 patients, with a prospective analysis of data from 244 patients with major trauma at our hospital and a retrospective analysis of data from 717 patients extracted from a database in the United States. The patients from our hospital constituted the model development cohort, and the patients from the database constituted the external validation cohort. The patients in the model development cohort were randomly divided into a training cohort and an internal validation cohort at a ratio of 8:2. The machine-learning algorithms used to train models included logistic regression, decision tree, extreme gradient boosting machine (eXGBM), neural network (NN), random forest, and light gradient boosting machine (LightGBM).

RESULTS

The incidence of sepsis for the model development cohort was 43.44%. Twelve predictors, including gender, abdominal trauma, open trauma, red blood cell count, heart rate, respiratory rate, injury severity score, sequential organ failure assessment score, Glasgow coma scale, smoking, total protein concentrations, and hematocrit, were used as features in the final model. Internal validation showed that the NN model had the highest area under the curve (AUC) of 0.932 (95% CI: 0.917-0.948), followed by the LightGBM and eXGBM models with AUCs of 0.913 (95% CI: 0.883-0.930) and 0.912 (95% CI: 0.880-0.935), respectively. In the external validation cohort, the eXGBM model (AUC: 0.891, 95% CI: 0.866-0.914) had the highest AUC value, followed by the LightGBM model (AUC: 0.886, 95% CI: 0.860-0.906), and the AUC value of the NN model was only 0.787 (95% CI: 0.751-0.829). Considering the predictive performance for both the internal and external validation cohorts, the LightGBM model had the highest score of 82, followed by the eXGBM (81) and NN (76) models. Thus, the LightGBM has emerged as the optimal model, and it was deployed online as an AI application.

CONCLUSIONS

This study develops and validates an AI application to effectively assess the susceptibility of patients with major trauma to sepsis. The AI application equips healthcare professionals with a valuable tool to promptly identify individuals at high risk of developing sepsis. This will facilitate clinical decision-making and enable early intervention.

Identification of a novel immune infiltration-related gene signature, MCEMP1, for coronary artery disease

Background

This study aims to identify a novel gene signature for coronary artery disease (CAD), explore the role of immune cell infiltration in CAD pathogenesis, and assess the cell function of mast cell-expressed membrane protein 1 (MCEMP1) in human umbilical vein endothelial cells (HUVECs) treated with oxidized low-density lipoprotein (ox-LDL).

Methods

To identify differentially expressed genes (DEGs) of CAD, datasets GSE24519 and GSE61145 were downloaded from the Gene Expression Omnibus (GEO) database using the R "limma" package with p < 0.05 and |log2 FC| > 1. Gene ontology (GO) and pathway analyses were conducted to determine the biological functions of DEGs. Hub genes were identified using support vector machine-recursive feature elimination (SVM-RFE) and least absolute shrinkage and selection operator (LASSO). The expression levels of these hub genes in CAD were validated using the GSE113079 dataset. CIBERSORT program was used to quantify the proportion of immune cell infiltration. Western blot assay and qRT-PCR were used to detect the expression of hub genes in ox-LDL-treated HUVECs to validate the bioinformatics results. Knockdown interference sequences for MCEMP1 were synthesized, and cell proliferation and apoptosis were examined using a CCK8 kit and Muse® Cell Analyzer, respectively. The concentrations of IL-1β, IL-6, and TNF-α were measured with respective enzyme-linked immunosorbent assay (ELISA) kits.

Results

A total of 73 DEGs (four down-regulated genes and 69 up-regulated genes) were identified in the metadata (GSE24519 and GSE61145) cohort. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results indicated that these DEGs might be associated with the regulation of platelet aggregation, defense response or response to bacterium, NF-kappa B signaling pathway, and lipid and atherosclerosis. Using SVM-RFE and LASSO, seven hub genes were obtained from the metadata. The upregulated expression of DIRC2 and MCEMP1 in CAD was confirmed in the GSE113079 dataset and in ox-LDL-treated HUVECs. The associations between the two hub genes (DIRC2 and MCEMP1) and the 22 types of immune cell infiltrates in CAD were found. MCEMP1 knockdown accelerated cell proliferation and suppressed cell apoptosis for ox-LDL-treated HUVECs. Additionally, MCEMP1 knockdown appeared to decrease the expression of inflammatory factors IL-1β, IL-6, and TNF-α.

Conclusions

The results of this study indicate that MCEMP1 may play an important role in CAD pathophysiology.

The 'analysis of gene expression and biomarkers for point-of-care decision support in Sepsis' study; temporal clinical parameter analysis and validation of early diagnostic biomarker signatures for severe inflammation andsepsis-SIRS discrimination

Introduction

Early diagnosis of sepsis and discrimination from SIRS is crucial for clinicians to provide appropriate care, management and treatment to critically ill patients. We describe identification of mRNA biomarkers from peripheral blood leukocytes, able to identify severe, systemic inflammation (irrespective of origin) and differentiate Sepsis from SIRS, in adult patients within a multi-center clinical study.

Methods

Participants were recruited in Intensive Care Units (ICUs) from multiple UK hospitals, including fifty-nine patients with abdominal sepsis, eighty-four patients with pulmonary sepsis, forty-two SIRS patients with Out-of-Hospital Cardiac Arrest (OOHCA), sampled at four time points, in addition to thirty healthy control donors. Multiple clinical parameters were measured, including SOFA score, with many differences observed between SIRS and sepsis groups. Differential gene expression analyses were performed using microarray hybridization and data analyzed using a combination of parametric and non-parametric statistical tools.

Results

Nineteen high-performance, differentially expressed mRNA biomarkers were identified between control and combined SIRS/Sepsis groups (FC>20.0, p<0.05), termed 'indicators of inflammation' (I°I), including CD177, FAM20A and OLAH. Best-performing minimal signatures e.g. FAM20A/OLAH showed good accuracy for determination of severe, systemic inflammation (AUC>0.99). Twenty entities, termed 'SIRS or Sepsis' (S°S) biomarkers, were differentially expressed between sepsis and SIRS (FC>2·0, p-value<0.05).

Discussion

The best performing signature for discriminating sepsis from SIRS was CMTM5/CETP/PLA2G7/MIA/MPP3 (AUC=0.9758). The I°I and S°S signatures performed variably in other independent gene expression datasets, this may be due to technical variation in the study/assay platform.

Multi-omic Profiling Reveals Early Immunological Indicators for Identifying COVID-19 Progressors

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a rapid response by the scientific community to further understand and combat its associated pathologic etiology. A focal point has been on the immune responses mounted during the acute and post-acute phases of infection, but the immediate post-diagnosis phase remains relatively understudied. We sought to better understand the immediate post-diagnosis phase by collecting blood from study participants soon after a positive test and identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. Additionally, in the lymphocyte compartment, CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. Importantly, the identification of these cellular and molecular immune changes occurred at the early stages of COVID-19 disease. These observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19.