Imaging mass cytometry-based characterisation of fibroblast subsets and their cellular niches in systemic sclerosis

Transcriptomic data demonstrated that fibroblasts are heterogeneous with functionally diverse subpopulations. Although fibroblasts are key effector cells of fibrotic diseases such as systemic sclerosis (SSc), they have not yet been characterised spatially at the cellular level. Here, we aimed to investigate fibroblast subpopulations using imaging mass cytometry (IMC) as a proteomic-based, spatially resolved omics approach.

We applied IMC to deconvolute the heterogeneity of 49 969 cells including 6501 fibroblasts at the single-cell level, to analyse their spatial distribution and to characterise their cellular niches in skin sections of patients with SSc and controls in situ.

We identified 13 different subpopulations of fibroblasts in SSc and control skin, the proportion increases in five fibroblast subpopulations (myofibroblasts, FAP^high, S1PR⁺, Thy1⁺;ADAM12^high;PU.1^high and ADAM12⁺;GLI1⁺ fibroblasts) and decreases in three subpopulations (TFAM^high, PI16⁺;FAP⁺ and Thy1⁺;ADAM12^low fibroblasts). Several fibroblast subpopulations demonstrated spatial enrichment and altered cellular interactions in SSc. The proportion of S1PR⁺-fibroblast positively correlated with more extensive skin fibrosis, whereas high numbers of PI16⁺;FAP^--fibroblasts were associated with milder skin fibrosis. The frequency of aberrant cellular interaction between S1PR⁺ and ADAM12⁺;GLI1⁺-fibroblasts also positively associated with the extent of skin fibrosis in SSc.

Using IMC, we demonstrated profound changes in composition and localisation of the majority of fibroblast subpopulations in SSc skin. These findings may provide a rationale for specific targeting of deregulated fibroblast subpopulations in SSc. Quantification of S1PR⁺-fibroblast and PI16⁺;FAP^--fibroblasts may offer potential for patient stratification according to severity of skin fibrosis.