Identification of two robust subclasses of sepsis with both prognostic and therapeutic values based on machine learning analysis

BACKGROUND: Sepsis is a heterogeneous syndrome with high morbidity and mortality. Optimal and effective classifications are in urgent need and to be developed. METHODS AND RESULTS: A total of 1,936 patients (sepsis samples, n=1,692; normal samples, n=244) in 7 discovery datasets were included to conduct weighted gene co-expression network analysis (WGCNA) to filter out candidate genes related to sepsis. Then, two subtypes of sepsis were classified in the training sepsis set (n=1,692), the Adaptive and Inflammatory, using K-means clustering analysis on 90 sepsis-related features. We validated these subtypes using 617 samples in 5 independent datasets and the merged 5 sets. Cibersort method revealed the Adaptive subtype was related to high infiltration levels of T cells and natural killer (NK) cells and a better clinical outcome. Immune features were validated by single-cell RNA sequencing (scRNA-seq) analysis. The Inflammatory subtype was associated with high infiltration of macrophages and a disadvantageous prognosis. Based on functional analysis, upregulation of the Toll-like receptor signaling pathway was obtained in Inflammatory subtype and NK cell-mediated cytotoxicity and T cell receptor signaling pathway were upregulated in Adaptive group. To quantify the cluster findings, a scoring system, called, risk score, was established using four datasets (n=980) in the discovery cohorts based on least absolute shrinkage and selection operator (LASSO) and logistic regression and validated in external sets (n=760). Multivariate logistic regression analysis revealed the risk score was an independent predictor of outcomes of sepsis patients (OR [odds ratio], 2.752, 95% confidence interval [CI], 2.234-3.389, P<0.001), when adjusted by age and gender. In addition, the validation sets confirmed the performance (OR, 1.638, 95% CI, 1.309-2.048, P<0.001). Finally, nomograms demonstrated great discriminatory potential than that of risk score, age and gender (training set: AUC=0.682, 95% CI, 0.643-0.719; validation set: AUC=0.624, 95% CI, 0.576-0.664). Decision curve analysis (DCA) demonstrated that the nomograms were clinically useful and had better discriminative performance to recognize patients at high risk than the age, gender and risk score, respectively. CONCLUSIONS: In-depth analysis of a comprehensive landscape of the transcriptome characteristics of sepsis might contribute to personalized treatments and prediction of clinical outcomes.