Predicting the immunity landscape and prognosis with an NCLs signature in liver hepatocellular carcinoma

• Published in: PloS one Vol. 19; no. 4; p. e0298775
• Main Authors: Ji, Zhangxin, Zhang, Chenxu, Yuan, Jingjing, He, Qing, Zhang, Xinyu, Yang, Dongmei, Xu, Na, Chu, Jun
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 25.04.2024; Public Library of Science (PLoS)
• Subjects: Analysis; Biology and life sciences; Biomarkers, Tumor - genetics; Cancer; Carcinoma, Hepatocellular - genetics; Carcinoma, Hepatocellular - immunology; Carcinoma, Hepatocellular - pathology; Care and treatment; Cell death; Chromatin; Diagnosis; Extracellular Traps - immunology; Extracellular Traps - metabolism; Female; Forecasts and trends; Gene expression; Gene Expression Regulation, Neoplastic; Genetic aspects; Genomes; Genomics; Health aspects; Hepatoma; Humans; Immunotherapy; Liver; Liver diseases; Liver Neoplasms - genetics; Liver Neoplasms - immunology; Liver Neoplasms - pathology; Male; Medicine and Health Sciences; Molecular mechanics; Neutrophils - immunology; Nomograms; Oncology, Experimental; Patient outcomes; Prognosis; Transcriptome; Tumor Microenvironment - immunology; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0298775

Activated neutrophils release depolymerized chromatin and protein particles into the extracellular space, forming reticular Neutrophil Extracellular Traps (NETs). This process is accompanied by programmed inflammatory cell death of neutrophils, known as NETosis. Previous reports have demonstrated that NETosis plays a significant role in immune resistance and microenvironmental regulation in cancer. This study sought to characterize the function and molecular mechanism of NETosis-correlated long non-coding RNAs (NCLs) in the prognostic treatment of liver hepatocellular carcinoma (LIHC). We obtained the transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and evaluated the expression of NCLs in LIHC. A prognostic signature of NCLs was constructed using Cox and Last Absolute Shrinkage and Selection Operator (Lasso) regression, while the accuracy of model was validated by the ROC curves and nomogram, etc. In addition, we analyzed the associations between NCLs and oncogenic mutation, immune infiltration and evasion. Finally, LIHC patients were classified into four subgroups based on consensus cluster analysis, and drug sensitivity was predicted. After screening, we established a risk model combining 5 hub-NCLs and demonstrated its reliability. Independence checks suggest that the model may serve as an independent predictor of LIHC prognosis. Enrichment analysis revealed a concentration of immune-related pathways in the high-risk group. Immune infiltration indicates that immunotherapy could be more effective in the low-risk group. Upon consistent cluster analysis, cluster subgroup 4 presented a better prognosis. Sensitivity tests showed the distinctions in therapeutic effectiveness among various drugs in different subgroups. Overall, we have developed a prognostic signature that can discriminate different LIHC subgroups through the 5 selected NCLs, with the objective of providing LIHC patients a more precise, personalized treatment regimen.