RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and is Associated with Disease Severity of Systemic Sclerosis [scRNA-seq]
The activation of Runt-related transcription factor 1 (RUNX1) in fibroblasts has been implicated in wound healing and fibrosis; however, the role of RUNX1 in the fibrotic progression of the autoimmune disease systemic sclerosis (SSc) is not known. Leveraging gene expression, genome-wide DNA methylation, and single-cell resolution data of SSc skin and fibroblast, we analyzed the impact of RUNX1 dysregulation in SSc dermal fibrosis. RUNX1 function was subsequently assessed using siRNA, pharmacologic inhibition, and CRISPR knockout in 2D and 3D fibroblasts cultures. Analysis of gene expression in multiple cohorts demonstrated an association between the severity of dermal fibrosis and the expression levels of RUNX1 in the skin of patients with SSc. Epigenomic analyses of methylation identified hypomethylated CpG sites proximal to the RUNX1 gene, implicating their potential role in the increased expression of RUNX1. Analysis of single-cell RNA-seq data from skin biopsies of individuals with SSc revealed that RUNX1 is higher in subpopulations of fibroblasts enriched in SSc, which are believed to contribute to fibrosis. RUNX1 CRISPR KO resulted in reduced alpha smooth muscle actin (a-SMA) expression. Inhibition of RUNX1 activity caused a reduction in fibroblast activation, contraction, extracellular matrix components, and proliferation rates including a reduction in SFRP4, LUM and COL1A1. This study is the first to demonstrate a potential role for RUNX1 in the pathogenesis of systemic sclerosis dermal fibrosis. RUNX1 is associated with more severe SSc fibrosis and is associated with a subpopulation of dermal fibroblasts implicated in fibrosis. Overall design: Skin fibroblasts isolated from SSc patients (n=2) were treated for 72 hours with either RUNX1 siRNA (Dharmacon, catalog ID E-003926-00-0010) or non-targeting control pool siRNA (NC, Dharmacon, D-001910-10-05). Single cell suspensions were then processed for scRNA-seq.