Identification and validation of mitochondrial ferroptosis and immune microenvironment-related hub biomarkers in liver cirrhosis by integrated bioinformatics analysis.

Abstract

BackgroundLiver cirrhosis represents a significant challenge to global public health. However, reliable biological markers for diagnosing liver cirrhosis are lacking in clinical practice.MethodsTranscriptome data from liver cirrhosis patients were acquired from the Gene Expression Omnibus database to identify coexpressed differentially expressed genes (DEGs). Mitochondria-related and ferroptosis-related genes were obtained from MitoCarta3.0 and FerrDB V2, respectively. Immune-related module genes were examined through Weighted Gene Co-Expression Network Analysis (WGCNA). By using WGCNA combined with machine learning methods, we identified immune-related biomarkers for liver cirrhosis. The immune cell infiltration was evaluated using CIBERSORTx, with core immune cell types further refined through LASSO regression and random forest. Hub biomarkers were validated using single-cell sequencing, with additional confirmation provided by histological staining and immunohistochemistry (IHC).ResultsThis study identified 2474 DEGs between liver cirrhosis and control groups. Intersection analysis with ferroptosis-related genes and mitochondria-related genes narrowed to 13 hub genes, from which machine learning selected 8 biomarkers. CIBERSORT and Wilcoxon tests revealed notable variations in the 12 immune cell types across the different groups. The WGCNA identified immune-related genes, with four immune-related biomarkers (DHODH, FXN, CS, and ISCU) identified as hub biomarkers. Integrated LASSO regression, random forest, and immune infiltration analyses pinpointed the core cells influencing disease progression. The relationship between the hub biomarkers and immune cells was validated by single-cell data analysis. ISCU expression was verified through IHC, consistent with our bioinformatics findings. Molecular docking identified three small molecules with potential effectiveness.ConclusionOur study identified mitochondrial ferroptosis-related genes (DHODH, FXN, CS, and ISCU) as pivotal biomarkers in liver cirrhosis progression and demonstrated a close connection with the immune microenvironment. These genes may serve as diagnostic indicators and therapeutic targets, thereby providing novel perspectives on the pathogenesis of liver cirrhosis.