Li Yi-Nan, Filla Tim, Györfi Andrea-Hermina, Liang Minrui, Devakumar Veda, Micu Alexandru, Chai Hongtao, Bergmann Christina, Pecher Ann-Christin, Henes Jörg, Moinzadeh Pia, Al-Gburi Suzan, Krieg Thomas, Kreuter Alexander, Wang Jiucun, Schett Georg, Homey Bernhard, Dietrich Sascha, Distler Jörg H W, Matei Alexandru-Emil
Department of Rheumatology, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany; Hiller Research Center, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
Department of Rheumatology, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany; Hiller Research Center, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
Ann Rheum Dis. 2025 Jul 1. doi: 10.1016/j.ard.2025.06.002.
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).
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.
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.
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.
空间未解析的转录组数据已识别出健康和疾病状态下功能上不同的成纤维细胞群体。然而，迄今为止，尚未能够以单细胞分辨率进行深入的原位转录谱分析。因此，我们旨在使用循环原位杂交（cISH）通过单细胞空间转录组学对这些群体进行分析。
我们使用cISH作为一种具有亚细胞分辨率的转录表型分析新方法，研究了系统性硬化症（SSc）患者和健康个体皮肤中的成纤维细胞亚群。使用具有邻域内核和空间尺度的构建聚集体（BANKSY）作为一种用于空间信息转录表型分析的新方法进行聚类。通过与不同SSc队列中的单细胞RNA测序整合，进一步验证了研究结果。
基于BANKSY的空间信息聚类识别出9个成纤维细胞（FB）亚群，其中SFRP2 + 网状真皮（RetD）FB和CCL19 + 非血管周（nonPV）FB是新的亚群，它们存在于特定的细胞微环境中，并显示出独特的基因表达谱。SFRP2 + RetD FB和CCL19 + nonPV FB以及COL8A1 + FB在SSc皮肤中的频率发生改变，并通过其转录谱、细胞相互作用和配体-受体分析表明，它们在细胞外基质释放和白细胞募集中发挥特定的促疾病作用。COL8A1 + FB的频率及其与单核细胞和B细胞的相互作用与SSc皮肤纤维化的进展相关。
我们基于cISH的空间解析转录组学方法识别出在SSc皮肤中失调且具有特定致病作用的新型成纤维细胞亚群。COL8A1 + FB及其免疫相互作用也可能作为皮肤纤维化未来进展的生物标志物。
