Abstract
Non-alcoholic fatty liver disease (MASLD) affects approximately 32.4% of adults globally, progressing from simple steatosis to non-alcoholic steatohepatitis (MASH), cirrhosis, and hepatocellular carcinoma (HCC). Alternative splicing (AS) is crucial for gene expression regulation, and its dysregulation is linked to disease progression. To identify early molecular signatures indicative of cirrhosis in MASLD, we analyzed RNA sequencing data from liver tissues of healthy controls (n = 10), MASLD patients (n = 9), and cirrhosis patients (n = 10) obtained from the SRA database (accession ERP146053). Utilizing SUVA for splicing event detection and k-means clustering, we examined dynamic changes in alternative splicing events and constructed regulatory networks of RNA-binding proteins (RBPs). Integration with immunological profiles enabled us to explore the interplay between splicing variants and immune responses during disease progression. We identified 671 differential alternative splicing events. Clustering revealed dynamic splicing patterns across disease stages, with two key patterns associated with DNA damage response (DDR) and epithelial-mesenchymal transition (EMT) processes, showing early progressive alterations correlating with disease severity. Twelve immune-related splicing events were significantly associated with changes in immune cell populations, highlighting their role in immune regulation during Liver disease progression. Additionally, 11 RBPs, including CELF5 and PCBP1, showed expression changes that correlate with splicing events associated with MASLD progression. Identifying early alternative splicing signatures and understanding RBP networks enhance our ability to predict disease progression and present potential therapeutic targets for early intervention. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12920-025-02233-1.