Spatially informed phenotyping by cyclic-in-situ-hybridisation identifies novel fibroblast populations and their pathogenic niches in systemic sclerosis

Li YN, Filla T, Györfi AH, Liang M, Devakumar V, Micu A, Chai H, Bergmann C, Pecher AC, Henes J, Moinzadeh P, Al-Gburi S, Krieg T, Kreuter A, Wang J, Schett G, Homey B, Dietrich S, Distler JH, Matei AE (2025)

Publication Type: Journal article

Publication year: 2025

Journal

Annals of the Rheumatic Diseases BMJ Publishing Group

DOI: 10.1016/j.ard.2025.06.002

Abstract

Objectives: Spatially nonresolved transcriptomic data identified several functionally distinct populations of fibroblasts in health and disease. However, in-depth transcriptional profiling in situ at the single-cell resolution has not been possible so far. We thus aimed to profile these populations by single-cell spatial transcriptomics using cyclic in situ hybridisation (cISH). Methods: We studied fibroblast subpopulations in the skin of systemic sclerosis (SSc) patients and heathy individuals using cISH as a novel approach for transcriptional phenotyping with subcellular resolution. Clustering was performed using Building Aggregates with a Neighbourhood Kernel and Spatial Yardstick (BANKSY) as a novel approach for spatially informed transcriptional phenotyping. The findings were further validated by integration with single-cell RNA sequencing in distinct SSc cohorts. Results: BANKSY-based spatially informed clustering identified 9 fibroblast (FB) subpopulations, with SFRP2+ reticular dermis (RetD) FB and CCL19+ nonperivascular (nonPV) FBs as novel subpopulations that reside in specific cellular niches and display unique gene expression profiles. SFRP2+ RetD FBs and CCL19+ nonPV FBs as well as COL8A1+ FBs display altered frequencies in SSc skin and play specific, disease-promoting roles for extracellular matrix release and leukocyte recruitment as revealed by their transcriptional profile, their cellular interactions, and ligand–receptor analyses. The frequencies of COL8A1+ FBs and their interactions with monocytic cells and B cells are associated with the progression of skin fibrosis in SSc. Conclusions: Our cISH-based, spatially resolved transcriptomic approach identified novel fibroblast subpopulations deregulated in SSc skin with specific pathogenic roles. COL8A1+ FBs and their immune interactions may also have potential as biomarkers for future progression of skin fibrosis.

Authors with CRIS profile

Christina Bergmann Department of Medicine 3 – Rheumatology and Immunology Georg Schett Lehrstuhl für Innere Medizin III

Involved external institutions

Universitätsklinikum Düsseldorf DE Germany (DE) Universitätsklinikum Tübingen DE Germany (DE) Universitätsklinikum Köln DE Germany (DE) Universität zu Köln DE Germany (DE) Fudan University / 复旦大学 CN China (CN)

How to cite

APA:

Li, Y.N., Filla, T., Györfi, A.H., Liang, M., Devakumar, V., Micu, A.,... Matei, A.E. (2025). Spatially informed phenotyping by cyclic-in-situ-hybridisation identifies novel fibroblast populations and their pathogenic niches in systemic sclerosis. Annals of the Rheumatic Diseases. https://doi.org/10.1016/j.ard.2025.06.002

MLA:

Li, Yi Nan, et al. "Spatially informed phenotyping by cyclic-in-situ-hybridisation identifies novel fibroblast populations and their pathogenic niches in systemic sclerosis." Annals of the Rheumatic Diseases (2025).

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