{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T17:21:00Z","timestamp":1791566460832,"version":"4.3.4"},"reference-count":47,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T00:00:00Z","timestamp":1783036800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>Autoimmune encephalitis (AE) represents a heterogeneous group of disorders characterized by immune-mediated attacks on neuronal antigens within the central nervous system (CNS), leading to diverse clinical manifestations and posing significant challenges in diagnosis and treatment. Recent advances in multi-omics technologies\u2014including genomics, transcriptomics, proteomics, metabolomics, and immunomics\u2014are beginning to provide unprecedented opportunities to unravel the complex immunopathophysiology of AE at a systems level. This review critically examines the application of integrated multi-omics approaches in AE research, with particular emphasis on immunological mechanisms underlying disease pathogenesis. We focus on: (i) the identification of potential diagnostic and prognostic biomarkers with rigorous validation frameworks; (ii) the elucidation of molecular heterogeneity underlying clinical variability, including B-cell clonal expansion, small-cohort evidence for T follicular helper (Tfh) expansion with inferred T follicular regulatory (Tfr) imbalance, and cytotoxic CD8+ T-cell-mediated neuronal injury in paraneoplastic\/intracellular-antigen contexts; (iii) the conceptual development of precision medicine strategies tailored to individual immunophenotypic profiles; and (iv) the critical appraisal of current evidence quality and methodological limitations. By synthesizing current findings, this article aims to establish a comprehensive immunological framework that supports the future advancement of personalized therapeutic interventions. The integration of multi-omics data offers a promising conceptual lens through which to understand the intricate immune-neuronal interactions driving AE, though substantial challenges in data standardization, clinical validation, and implementation remain to be addressed.<\/jats:p>","DOI":"10.3389\/fimmu.2026.1893602","type":"journal-article","created":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T05:39:42Z","timestamp":1783057182000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Multi-omics integration in autoimmune encephalitis: from novel biomarker discovery to precision therapeutic strategies"],"prefix":"10.3389","volume":"17","author":[{"given":"Xudong","family":"Chen","sequence":"first","affiliation":[{"name":"Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School","place":["Yancheng, 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