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

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.