Multi-omic analysis reveals molecular subtypes with distinct immunological phenotypes in SLE [RNA-Seq]

Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease characterized by variability in clinical manifestations and underlying molecular mechanisms. To investigate this heterogeneity, we performed integrative multi-omic profiling—including epigenomic (EM-seq), transcriptomic (RNA-seq), and proteomic (Olink) analyses—on whole blood samples from over 700 SLE patients enrolled in two Phase III clinical trials. Using this approach, we identified three stable molecular endotypes of SLE, providing a framework for understanding disease subtypes and informing precision medicine strategies.