Single-cell epigenomic dysregulation of Systemic Sclerosis fibroblasts via CREB1/EGR1 axis in self-assembled human skin equivalents

Abel, T. R.; Kosarek, N. N.; Parvizi, R.; Jarnagin, H. C.; Torres, G. M.; Bhandari, R.; Huang, M.; Toledo, D.; Smith, A.; Popovich, D.; Mariani, M. P.; Yang, H.; Wood, T. A.; Garlick, J.; Pioli, P. A.; Whitfield, M. L.

doi:10.1101/2024.03.22.586316

bioRxiv · 10.1101/2024.03.22.586316

Single-cell epigenomic dysregulation of Systemic Sclerosis fibroblasts via CREB1/EGR1 axis in self-assembled human skin equivalents

Abel, T. R.·Kosarek, N. N.·Parvizi, R.·Jarnagin, H. C.·Torres, G. M.·Bhandari, R.·Huang, M.·Toledo, D.·Smith, A.·Popovich, D.·Mariani, M. P.·Yang, H.·Wood, T. A.·Garlick, J.·Pioli, P. A.·Whitfield, M. L.

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Abstract

Systemic sclerosis (SSc) is an autoimmune disease characterized by skin fibrosis, internal organ involvement and vascular dropout. We previously developed and phenotypically characterized an in vitro 3D skin-like tissue model of SSc, and now analyze the transcriptomic (scRNA-seq) and epigenetic (scATAC-seq) characteristics of this model at single-cell resolution. SSc 3D skin-like tissues were fabricated using autologous fibroblasts, macrophages, and plasma from SSc patients or healthy control (HC) donors. SSc tissues displayed increased dermal thickness and contractility, as well as increased -SMA staining. Single-cell transcriptomic and epigenomic analyses identified keratinocytes, macrophages, and five populations of fibroblasts (labeled FB1 - 5). Notably, FB1 APOE-expressing fibroblasts were 12-fold enriched in SSc tissues and were characterized by high EGR1 motif accessibility. Pseudotime analysis suggests that FB1 fibroblasts differentiate from a TGF-{beta}1-responsive fibroblast population and ligand-receptor analysis indicates that the FB1 fibroblasts are active in macrophage crosstalk via soluble ligands including FGF2 and APP. These findings provide characterization of the 3D skin-like model at single cell resolution and establish that it recapitulates subsets of fibroblasts and macrophage phenotypes observed in skin biopsies.

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Abel, T. R., Kosarek, N. N., Parvizi, R., Jarnagin, H. C., Torres, G. M., Bhandari, R., Huang, M., Toledo, D., Smith, A., Popovich, D., Mariani, M. P., Yang, H., Wood, T. A., Garlick, J., Pioli, P. A., Whitfield, M. L.. 2024-03-27. Single-cell epigenomic dysregulation of Systemic Sclerosis fibroblasts via CREB1/EGR1 axis in self-assembled human skin equivalents. https://doi.org/10.1101/2024.03.22.586316

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