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Each cohort was compared with age\u2010matched and sex\u2010matched non\u2010inflammatory neurological disorder controls. Differentially abundant proteins (false discovery rate [FDR]\u2009&lt;\u20090.05) and enriched pathways were identified using Reactome. Selected proteins were validated using targeted mass spectrometry (selected reaction monitoring or high\u2010resolution multiple reaction monitoring).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Encephalitis showed increased immunoglobulin and acute\u2010phase proteins, with reduced glycolysis, synaptic, and extracellular matrix proteins. AGS demonstrated increased interferon signalling, Toll\u2010like receptor pathways, and synaptic proteins, with reduced neural structural and extracellular matrix proteins. ASD exhibited increased extracellular matrix organization and oxidative protection proteins, with decreased haemostatic and stress response proteins. Complement and innate immune pathways were enriched across all cohorts, with increased abundance of C1S, C1R, CFH, and C4A.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Interpretation<\/jats:title>\n                    <jats:p>This hypothesis\u2010generating study shows shared complement activation across encephalitis, AGS, and ASD, which suggests complement dysregulation as a common neuroimmune mechanism and potential biomarker in childhood neuroinflammation.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1111\/dmcn.70467","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T10:49:29Z","timestamp":1787136569000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Shared dysregulation of complement and phosphorylation pathways in the cerebrospinal fluid of encephalitis, Aicardi\u2013Gouti\u00e8res syndrome, and autism"],"prefix":"10.1111","author":[{"given":"Omar H.","family":"Shadid","sequence":"first","affiliation":[{"name":"School of Medical Sciences and Discipline of Child and Adolescent Health, Faculty of Medicine and Health The University of Sydney  Sydney New South Wales Australia"},{"name":"Cell Signalling Group, Children's Medical Research Institute University of Sydney  Westmead New South Wales Australia"},{"name":"Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health University of Sydney  Sydney New South Wales Australia"},{"name":"The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter G.","family":"Hains","sequence":"additional","affiliation":[{"name":"Cell Signalling Group, Children's Medical Research Institute University of Sydney  Westmead New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4633-4316","authenticated-orcid":false,"given":"Velda X.","family":"Han","sequence":"additional","affiliation":[{"name":"Khoo Teck Puat\u2010National University Children's Medical Institute National University Health System  Singapore"},{"name":"Department of Paediatrics, Yong Loo Lin School of Medicine National University of Singapore  Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingya","family":"Yan","sequence":"additional","affiliation":[{"name":"School of Mathematical and Physical Sciences University of Technology Sydney  Sydney New South Wales Australia"},{"name":"Department of Biochemistry The Children's Hospital at Westmead  Westmead New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Griffiths","sequence":"additional","affiliation":[{"name":"School of Medical Sciences and Discipline of Child and Adolescent Health, Faculty of Medicine and Health The University of Sydney  Sydney New South Wales Australia"},{"name":"Child and Adolescent Health Research Centre, Faculty of Medicine and Health University of Sydney  Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ignatius","family":"Pang","sequence":"additional","affiliation":[{"name":"Bioinformatics Core Facility, Children's Medical Research Institute University of Sydney  Westmead New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sushil","family":"Bandodkar","sequence":"additional","affiliation":[{"name":"Department of Biochemistry The Children's Hospital at Westmead  Westmead New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7878-0313","authenticated-orcid":false,"given":"Phillip J.","family":"Robinson","sequence":"additional","affiliation":[{"name":"School of 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