Autoantibody reactome analysis reveals diagnostic biomarkers and molecular classification for relapsing polychondritis

The lack of effective biomarkers for relapsing polychondritis (RP) poses a significant challenge in its early diagnosis and treatment. This study aimed to identify novel autoantibodies and elucidate the pathogenesis and molecular heterogeneity of RP. Plasma samples from 467 RP patients, 164 healthy controls (HCs), and 186 disease controls (DCs) were analysed using 2 sequential microarrays and enzyme-linked immunosorbent assay to sequentially discover, validate, and verify new autoantibodies. Machine learning and differential analysis were used to identify diagnosis-specific autoantibodies and their correlation with disease activity, recurrence, and remission. The RP group had 1344 elevated autoantibodies, discriminating RP patients from HCs. These antigenic targets were associated with pathways involving autoimmune responses, infections, and cardiovascular lesions. Two molecular subtypes characterised by distinct organ involvement and prognosis highlighted the heterogeneity of RP. Notably, 14 new autoantibodies were identified, which differentiated RP versus HCs and DCs with a sensitivity of 41% and 49.7% and a specificity of 91.7% and 90.5%, respectively. Among them, 6 autoantibodies showed better diagnostic performance and were consistently verified. Specifically, anti-C4B was positively correlated with disease activity, and increased anti-KRT16 predicted RP recurrence within 1 year. In addition, anti-C4B, anti-FNBP4, and anti-KRT10 decreased from acute attack to remission. Furthermore, the deposition of C4B protein in tracheal tissues, coupled with its reduction in plasma of RP patients, indicated that abnormal complement activation might be related to the pathological mechanism of RP. The 14 autoantibodies promoted a noninvasive early detection of RP, predicted disease recurrence and provided new insights into the understanding of RP pathogenesis.