Multi-omics-driven biomarker discovery in autoimmune diseases: a comprehensive review

Autoimmune diseases (ADs) exhibit complex heterogeneity and dynamic pathological mechanisms. Traditional biomarkers face numerous challenges in the diagnosis and treatment of ADs. However, the rapid development of multi-omics technologies and bioinformatics has not only deepened the understanding of the pathogenesis of ADs but also identified many novel diagnostic and therapeutic biomarkers with good diagnostic performance. These biomarkers are now beginning to overcome these limitations. This review systematically explores the discovery of novel biomarkers driven by multi-omics technologies such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomics, in response to the limitations of traditional biomarkers. It emphasises the significant importance of discovering novel biomarkers through multi-omics in the diagnosis and treatment of ADs, and proposes a concept from omics analysis to solving clinical problems, providing new directions for the diagnosis and treatment of ADs.