Synovial tissue atlas in juvenile idiopathic arthritis reveals pathogenic niches associated with disease severity
Chrissy Bolton, Christopher B. Mahony, Elizabeth Clay, Patricia Reis Nisa, Søren Lomholt, Annie Hackland, Paulynn Suyin Chin, Charlotte G. Smith, Vicky Alexiou, Huong D. Nguyen, Manigandan Thyagarajan, Zishan Sheikh, Penny Davis, Samantha Chippington, Sandrine Compeyrot‐Lacassagne, Sunit Davda, Charlene Foley, Inga Z Turtsevich, Benjamin Ingledow, Klaudia Kupiec, James Kelly, Megan M. Hanlon, Edward F. DiCarlo, Megan M. Hanlon, Samantha Smith, Stephen Eyre, Georgiana Neag, Samuel Kemble, Roopa Madhu, Mukta G. Palshikar, Ilya Korsunsky, Ce Gao, Miles Tran, Calliope A. Dendrou, Christopher D. Buckley, Mark Coles, Karim Raza, Mark C. Coles, Ellen M. Gravallese, Andrew Filer, Kevin Wei, Eslam Al‐Abadi, Elizabeth C. Rosser, Lucy R. Wedderburn, Adam P. Croft, H. Adams, Hussein Al‐Mossawi, Rehana Begum, Ian Beh, Catherine Cotter, J. Mordaunt Crook, Serena Cruickshank-Hull, Catherine Cotter, L. Fuller, Gunnar Gottschalk, Nadège Haouidji-Javaux, Ruth Howman, Kimme L Hyrich, Maryam Imran, P Jenkins, Kelsey Jones, Maryam Imran, Kerry Leslie, Neelam Khan, Brian D. Marsden, Lucy‐Jayne Marsh, Diarmuid McLaughlin, Alyssia McNeece, Rafeeq Muhammed, Chadwick Pils, Emily Powell, Sugrah Sultan, Chadwick Pils, Holm H. Uhlig, Qiong Wu, Laura Threadgold, Holm H. Uhlig, Qiong Wu, the CLUSTER Champions
Abstract
Precision application of targeted therapies is urgently needed to improve long-term clinical outcomes for children affected by inflammatory arthritis, known as juvenile idiopathic arthritis (JIA). Progress has been hampered by our limited understanding of the cellular basis of inflammation in the target tissue of the disease, the synovial membrane. Here, we analyzed biopsies from the inflamed joints of treatment-naïve children with JIA, early in the course of their disease, using single-cell RNA sequencing, multiplexed immunofluorescence, and spatial transcriptomics to establish a cellular atlas of the JIA synovium. We identified distinct spatial tissue niches, composed of specific stromal and immune cell populations. In addition, we localized genes linked to arthritis severity and disease risk to effector cell populations, including tissue resident SPP1 + macrophages and fibrin-associated myeloid cells. Combined analyses of synovial fluid and peripheral blood from matched individuals revealed differences in cellular composition, signaling pathways, and transcriptional programs across these distinct anatomical compartments. Furthermore, our analysis revealed several pathogenic cell populations that are shared with adult-onset inflammatory arthritis, as well as age-associated differences in tissue vascularity, prominence of innate immunity, and enrichment of TGF-β–responsive stromal subsets that up-regulate expression of disease risk–associated genes. Overall, our findings demonstrate the need for age-specific analyses of synovial tissue pathology to guide targeted treatment strategies in JIA.