Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases Ilya Korsunsky1-5,15, Kevin Wei1,15, Mathilde Pohin6,15, Edy Y. Kim7,8,15, Francesca Barone9,15, Joyce B. Kang1-5, Matthias Friedrich6, Jason Turner9, Saba Nayar9,10, Benjamin A. Fisher9,10, Karim Raza9,, Jennifer L. Marshall9, Adam P. Croft9, Lynette M. Sholl11, Marina Vivero11, Ivan O. Rosas12, Simon J. Bowman9,10, Mark Coles6, Andreas P. Frei13, Kara Lassen13, Andrew Filer9,10, Fiona Powrie6,16, Christopher D. Buckley9,10,16, Michael B. Brenner1,7,16, Soumya Raychaudhuri1-5,14,16 1Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA. 2Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA. 3Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA. 4Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. 5Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. 6Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, United Kingdom 7Harvard Medical School, Boston, MA 02115, USA 8Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA 9Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, B15 2WD, UK. 10NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom. 11Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA. 12Department of Medicine Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Dallas, TX, USA. 13Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland 14Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK. 15These authors contributed equally 16These authors jointly supervised this work Pro-inflammatory fibroblasts are critical to pathogenesis in rheumatoid arthritis, inflammatory bowel disease, interstitial lung disease, and Sjögren’s syndrome, and represent a novel therapeutic target for chronic inflammatory disease. However, the heterogeneity of fibroblast phenotypes, exacerbated by the lack of a common cross-tissue taxonomy, has limited the understanding of which pathways are shared by multiple diseases. To investigate, we profiled patient-derived fibroblasts from inflamed and non-inflamed synovium, intestine, lung, and salivary glands with single-cell RNA-sequencing. We integrated all fibroblasts into a multi-tissue atlas to characterize shared and tissue-specific phenotypes. Two shared clusters, CXCL10+CCL19+ immune-interacting and SPARC+COL3A1+ vascular-interacting fibroblasts were expanded in all inflamed tissues and additionally mapped to dermal analogues in a public atopic dermatitis atlas. We further confirmed these human pro-inflammatory fibroblasts in animal models of lung, joint, and intestinal inflammation. This work represents the first cross-tissue, single-cell fibroblast atlas revealing shared pathogenic activation states across four chronic inflammatory diseases.