Unsupervised clustering of clinical and laboratory features of systemic lupus erythematosus: insights from a multicentre cohort

OBJECTIVE: This study explored the relationship between clinical phenotypes and immuno-molecular features of systemic lupus erythematosus (SLE) using unsupervised machine learning and multi-omics integration. METHODS: A multicentre cohort of 1065 SLE patients from five teaching hospitals was studied. Unsupervised clustering was performed using integrated clinical and laboratory data to identify distinct phenotypic clusters. Multi-omics profiling, including proteomics and transcriptomics, was conducted for each cluster, comparing with healthy controls. In addition, 899 patients were prospectively followed for over 1 year to assess therapeutic responses and remission outcomes. RESULTS: regulatory T cells. Transcriptomic and proteomic analyses confirmed distinct molecular signatures and cluster-specific enrichment of biological pathways. Key molecule apolipoprotein A4 was validated using enzyme-linked immunosorbent assay. Regarding therapeutic outcomes at 1 year follow-up, Cluster 2 had the highest proportions achieving lupus low disease activity state (46.42%) and tapering glucocorticoids. Cyclophosphamide use was associated with greater clinical improvement (r=0.284; p=0.023) in Cluster 3, while in Cluster 5, rituximab use was associated with favourable responses (r=0.286; p=0.019). CONCLUSIONS: We identified five SLE clusters with distinct clinical, immunological features and treatment outcomes, demonstrating an intrinsic link between clinical involvement and immune-inflammatory alterations.