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

作者：Yinan Li, Tim Filla, Andrea‐Hermina Györfi, Minrui Liang, Veda Devakumar, Alexandru Micu, Hongtao Chai, Christina Bergmann, Ann‐Christin Pecher, Jörg Henes, Pia Moinzadeh, Suzan Al-Gburi, Thomas Krieg, Alexander Kreuter, Jiucun Wang, Georg Schett, Bernhard Homey, Sascha Dietrich, Jörg H. W. Distler, Alexandru‐Emil Matei · 发表于：Annals of the Rheumatic Diseases · 年份：2025 · DOI：10.1016/j.ard.2025.06.002 · 被引用次数：6 · 研究领域：Systemic Sclerosis and Related Diseases、Single-cell and spatial transcriptomics、Inflammatory Myopathies and Dermatomyositis

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+ ...