Objective To explore “state and target” pathological mechanism of sepsis by comprehensively analyzing the single-cell transcriptomics and transcriptomic datasets related to sepsis, construct the prognostic model for “state and target” of sepsis, and explore potential target Chinese medicines and active ingredients. Methods Differential expression gene analysis and venn diagram analysis were used to identify “state and target” of sepsis related genes. Key module genes were obtained using the random walk algorithm through the connectivity of the protein-protein interaction (PPI) network. Gene ontology (GO) biological process (BP) and Kyoto encyclopedia of genes and genomes (KEGG) were used to analyze the biological functions of key module genes. To explore the role of “state and target” of sepsis related genes by single-cell transcriptome analysis. A prognostic model for “state and target” of sepsis was constructed using gene expression data and clinical survival data from sepsis patients. The expression levels of prognostic genes for “state and target” of sepsis were validated by constructing sepsis mouse model and real-time quantitative polymerase chain reaction (RT-PCR). Through reverse network pharmacology, potential targeted traditional Chinese medicines and their active components were screened, and molecular docking was used to verify the binding performance between active ingredients and prognostic targets. Results A total of 70 genes related to “toxic state” of sepsis, 67 genes related to “stasis state” of sepsis and 54 genes related to “deficiency state” of sepsis were obtained. The key module genes of “toxic state” of sepsis were closely related to inflammation, the key module genes of “stasis state” of sepsis were closely related to coagulation, and the key module genes of “deficiency state” of sepsis were closely related to cell homeostasis. AUCell score showed that monocyte had the highest score for “toxic state” and “deficiency state” of sepsis. Platelet had the highest score for “stasis state” of sepsis. The activities of metabolic and inflammatory related genes and pathways were significantly up-regulated in monocytes with high “toxic state” score. Platelet activation and coagulation/thrombosis related genes and pathways were significantly up-regulated in platelet with high “stasis state” score. Compared with control group, there were a large number of down-regulated genes in monocytes of sepsis patients, which were involved in antigen presentation, cell energy metabolism, cell cycle, protein synthesis, etc. The prognostic model for “state and target” of sepsis constructed based on eight targets [interleukin-1 receptor type 2 (IL1R2), ADP ribosylation factor like GTPase 4C (ARL4C), cytochrome C oxidase subunit 7B (COX7B), eukaryotic translation initiation factor 2 subunit gamma (EIF2S3), immediate early response 3 (IER3), LSM1 homolog (LSM1), paired basic amino acid cleaving enzyme (FURIN) and ankyrin repeat domain-containing protein 9 (ANKRD9)] had good prognostic predictive ability, and the expression levels of these genes were validated using animal experiments and RT-PCR. Based on the bioinformatics analysis tool for molecular mechanism of traditional Chinese medicine (BATMAN-TCM) database and database of constituents absorbed into the blood and metabolites of traditional Chinese medicine (DCABM-TCM), reverse network pharmacology analysis had screened multiple Chinese herbal medicines with effects of clearing heat and detoxifying, activating blood and resolving stasis, and reinforcing healthy qi and their active ingredients entering the blood. Molecular docking showed that representative active ingredients have good binding properties with prognostic targets. Conclusion Activation of inflammatory response driven by monocyte metabolic reprogramming may be the main pathological mechanism of “toxic state” of sepsis. Platelet activation-coagulation/thrombosis may be the main pathological mechanism of “stasis state” of sepsis. Monocyte dysfunction-immunosuppression may be the main pathological mechanism of “deficiency state” of sepsis. A model based on eight genes can serve as a risk prediction model for the prognosis of “state and target” of sepsis.

sepsis  /  “state and target” theory  /  single-cell transcriptome  /  transcriptome  /  prognostic model  /  animal model  /  reverse network pharmacology