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This diversity cannot be explained by a single pathogenic mechanism or by conventional serological categories alone. Here, we synthesize evidence that autoimmunity is shaped by interacting molecular and cellular regulatory layers, including immunometabolic rewiring, epigenetic remodeling, posttranscriptional regulation, and functional reprogramming of immune and tissue\u2010resident cells. These processes influence pathogenic T\u2010cell and B\u2010cell differentiation, myeloid activation, stromal and epithelial dysfunction, tissue\u2010specific inflammation, and intercellular communication. We further discuss how multidimensional readouts, including metabolites, methylation and chromatin signatures, RNA\u2010based markers, and reprogrammed immune\u2010cell phenotypes, may support diagnosis, disease\u2010activity assessment, prognosis, and therapeutic stratification. From a therapeutic perspective, this framework supports a shift from broad immunosuppression toward mechanism\u2010matched interventions targeting metabolic vulnerabilities, epigenetic regulators, RNA\u2013control pathways, and pathogenic cellular states, including emerging cell\u2010based approaches. We propose that ADs can be viewed as dynamic network disorders in which molecular mechanisms, biomarkers, and therapeutic opportunities are closely connected. Integrating longitudinal multiomics, single\u2010cell and spatial profiling, and standardized biomarker validation may help translate autoimmune heterogeneity into actionable precision\u2010medicine strategies for more individualized care.<\/jats:p>","DOI":"10.1002\/mco2.70905","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T07:22:01Z","timestamp":1788420121000},"source":"Crossref","is-referenced-by-count":0,"title":["Autoimmunity: Molecular Mechanisms, Biomarkers, and Therapeutic Opportunities"],"prefix":"10.1002","volume":"7","author":[{"given":"Jialong","family":"Kuang","sequence":"first","affiliation":[{"name":"Department of Pediatrics Affiliated Hospital of Zunyi Medical University  Zunyi China"},{"name":"Guizhou Children's Hospital  Zunyi China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yin","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Pediatrics Affiliated Hospital of Zunyi Medical 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