Population-level single-cell genomics reveals conserved gene programs in systemic juvenile idiopathic arthritis

Systemic autoimmune and autoinflammatory diseases are characterized by genetic and cellular heterogeneity. While current single-cell genomics methods provide insights into known disease subtypes, these analysis methods do not readily reveal novel cell-type perturbation programs shared amongst distinct patient subsets. Here, we performed single-cell RNA-Seq of PBMCs of systemic juvenile idiopathic arthritis (SJIA) patients with diverse clinical manifestations, including macrophage activation syndrome (MAS) and lung disease (LD). We introduced two new computational frameworks called UDON and SATAY-UDON which define new patient subtypes based on their underlying disrupted cellular programs as well as associated biomarkers or clinical features. Among twelve independently identified subtypes, this analysis uncovered a novel complement and interferon activation program identified in SJIA-LD monocytes. Extending these analyses to adult and pediatric lupus patients found new but also shared disease programs with SJIA, including interferon and complement activation. Finally, supervised comparison of these programs in a compiled single-cell pan-immune atlas of over 1,000 healthy donors found a handful of normal healthy donors with evidence of early inflammatory activation in subsets of monocytes and platelets, nominating new possible biomarkers for early disease detection. Thus, integrative pan-immune single-cell analysis resolved new conserved gene programs underlying inflammatory disease pathogenesis and associated complications.