Glycoproteomic Signatures of IgG Subclass N ‐Glycosylation Reveal Molecular Endotypes in Idiopathic Inflammatory Myopathies

ABSTRACT

Idiopathic inflammatory myopathies (IIMs) are heterogeneous autoimmune diseases for which robust molecular classifiers are lacking. In this retrospective cross‐sectional study, we profiled immunoglobulin G (IgG) subclass‐specific N ‐glycosylation in IIMs and investigated their associations with clinical phenotypes and histopathological features. Using liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) with an electron‐transfer/higher energy collisional dissociation‐stepped collision energy higher energy collisional dissociation (EThcD‐sceHCD) fragmentation strategy, we analyzed plasma samples from 145 patients with IIMs and 52 age‐ and sex‐comparable healthy controls (HCs). Compared with HCs, patients with IIMs showed increased core fucosylation and significant alterations in 13 site‐specific IgG glycopeptides. Unsupervised clustering identified three glycosylation‐defined endotypes with muscle‐, cutaneous‐, and joint‐dominant phenotypes, each characterized by distinct glycoform patterns, clinical manifestations, and serological profiles. Specific IgG2 glycoforms were associated with markers of muscle injury and membrane attack complex (C5b‐9) deposition, suggesting a link between IgG glycosylation and complement‐mediated tissue damage. A seven‐glycopeptide multinomial logistic regression model and endotype‐specific nomograms were developed for exploratory cluster assignment, with moderate discrimination in the internal validation cohort (macro‐averaged area under the curve [macro‐AUC], 0.74). These findings identify IgG subclass‐specific N ‐glycosylation as a molecular layer underlying IIM heterogeneity beyond conventional clinical classification and provide a glycoproteomic framework for biomarker‐driven stratification, histopathological interpretation, and future mechanistic investigation.