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This study focuses on thyroid eye disease (TED), a representative AITD, to provide a deeper insight into its neural mechanism. We first combined resting\u2010state functional magnetic resonance imaging (rs\u2010fMRI) data from a retrospective cohort of 116 TED patients with transcriptomic data from the Allen Human Brain Atlas. The analysis of rs\u2010fMRI data demonstrated significant alterations in frontal, parietal, subcortical, and brainstem regions in TED. By integrating rs\u2010fMRI data with regional transcriptomic profiles derived from the postmortem Allen Human Brain Atlas, enabling region\u2010level transcriptional inference, we revealed enriched pathways related to synaptic signaling, neurovascular regulation, and immune activation. Tissue and cellular level enrichment further showed\u00a0close association with the cortex and neurons. Key neuroimaging findings identified in the retrospective cohort were subsequently validated in an independent prospective cohort of TED patients and healthy controls (TED: 39; HC: 42) using paired rs\u2010fMRI and peripheral blood RNA sequencing data, which identified significant associations between immune cell infiltration and neural activity patterns. Collectively, these findings delineate coordinated brain\u2013immune associations in TED and generate hypotheses regarding neuroimmune interactions in AITD.<\/jats:p>","DOI":"10.1002\/advs.202523609","type":"journal-article","created":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T19:38:35Z","timestamp":1772998715000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Transcriptomic and Neuroimaging Decoding of Brain\u2010Immune Crosstalk in Thyroid Eye Disease"],"prefix":"10.1002","volume":"13","author":[{"given":"Haiyang","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Eye Health Department of Ophthalmology Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine  Shanghai China"},{"name":"Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology  Shanghai 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