Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis [scRNA-Seq]

recision use of targeted therapies is urgently needed to improve long-term clinical outcomes for children affected by inflammatory arthritis, known as Juvenile Idiopathic Arthritis. Progress has been obstructed by a lack of understanding of the cellular basis of joint inflammation in children, given the difficulties in obtaining and studying synovial tissue itself. To this end, we combine single-cell RNA-sequencing, multiplexed immunofluorescence imaging and spatial transcriptomics to define the cellular and transcriptomic landscape of the synovium in children with Juvenile Idiopathic Arthritis. We identify spatial niches of resident and infiltrating cell populations that correlate with the degree of inflammation, and gene programs associated with arthritis severity. Combined with analyses of synovial fluid and peripheral blood from the same children, we distinguish differences in cellular composition, signalling pathways and transcriptional programs across anatomical compartments. Whilst we identify several pathogenic populations shared with adult-onset arthritis, our analyses highlight increased vascularity of the inflamed developing joint and TGFb-driven stromal subsets that upregulate expression of disease risk-associated genes. Overall, these findings illustrate the need for treatment algorithms informed by a tissue-based classification of arthritis. Overall design: To determine the molecular and cellular architecture of the inflamed joint in JIA, nineteen children underwent minimally invasive ultrasound-guided biopsies of the synovium, early in the course of their disease. Matched peripheral blood and synovial fluid samples were also collected. All participants were naïve to disease-modifying anti-rheumatic drugs (DMARDs) for the treatment of their arthritis. Participants with four ILAR subtypes of JIA were included, of whom 90% had oligoarticular or Rheumatoid Factor-negative JIA. Biopsy tissue samples were disaggregated and underwent 5' single-cell RNA-sequencing (scRNA-seq), combined with parallel histopathological assessment of formalin-fixed paraffin-embedded sections, or analysed with spatial profiling technologies (transcriptomics, multiplexed imaging). scRNA-seq was also performed on matched samples of peripheral blood mononuclear cells (PBMC) and synovial fluid mononuclear cells (SFMC), with paired detection of 137 expressed surface proteins. UPDATE: [Sep-28-2025] The GSE278962_meta_new.tsv file was updated.