Identification of neutrophil extracellular trap-related biomarkers in non-alcoholic fatty liver disease through machine learning and single-cell analysis

• Published in: Scientific reports Vol. 14; no. 1; pp. 21085 - 19
• Main Authors: Fang, Zhihao, Liu, Changxu, Yu, Xiaoxiao, Yang, Kai, Yu, Tianqi, Ji, Yanchao, Liu, Chang
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10-09-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/337; 692/163; 692/420; Bioinformatics; Biomarker; Biomarkers; Biomarkers - metabolism; Cell interactions; Cirrhosis; Diagnosis; Extracellular Traps - metabolism; Fatty liver; Gene Expression Profiling; Hepatocytes; Humanities and Social Sciences; Humans; Learning algorithms; Leukocytes (neutrophilic); Liver; Liver diseases; Machine Learning; Metabolic pathways; Metabolism; Microenvironments; multidisciplinary; Neutrophil extracellular traps (NETs); Neutrophils; Neutrophils - metabolism; Non-alcoholic fatty liver disease; Non-alcoholic Fatty Liver Disease - genetics; Non-alcoholic Fatty Liver Disease - metabolism; Non-alcoholic Fatty Liver Disease - pathology; Science; Science (multidisciplinary); Single-Cell Analysis - methods; Single-cell RNA-seq; Transcriptome; Transcriptomics; Biomarker; Neutrophil extracellular traps (NETs); Non-alcoholic fatty liver disease; Single-cell RNA-seq; Bioinformatics; Machine learning
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-72151-2

Non-alcoholic Fatty Liver Disease (NAFLD), noted for its widespread prevalence among adults, has become the leading chronic liver condition globally. Simultaneously, the annual disease burden, particularly liver cirrhosis caused by NAFLD, has increased significantly. Neutrophil Extracellular Traps (NETs) play a crucial role in the progression of this disease and are key to the pathogenesis of NAFLD. However, research into the specific roles of NETs-related genes in NAFLD is still a field requiring thorough investigation. Utilizing techniques like AddModuleScore, ssGSEA, and WGCNA, our team conducted gene screening to identify the genes linked to NETs in both single-cell and bulk transcriptomics. Using algorithms including Random Forest, Support Vector Machine, Least Absolute Shrinkage, and Selection Operator, we identified ZFP36L2 and PHLDA1 as key hub genes. The pivotal role of these genes in NAFLD diagnosis was confirmed using the training dataset GSE164760. This study identified 116 genes linked to NETs across single-cell and bulk transcriptomic analyses. These genes demonstrated enrichment in immune and metabolic pathways. Additionally, two NETs-related hub genes, PHLDA1 and ZFP36L2, were selected through machine learning for integration into a prognostic model. These hub genes play roles in inflammatory and metabolic processes. scRNA-seq results showed variations in cellular communication among cells with different expression patterns of these key genes. In conclusion, this study explored the molecular characteristics of NETs-associated genes in NAFLD. It identified two potential biomarkers and analyzed their roles in the hepatic microenvironment. These discoveries could aid in NAFLD diagnosis and management, with the ultimate goal of enhancing patient outcomes.