Systemic sclerosis (SSc) is a rare autoimmune disease characterized by vasculopathy and progressive fibrosis of the skin and internal organs. Individuals with SSc often suffer from chronic acid reflux and dysphagia due to loss of esophageal motility. However, the pathogenesis of esophageal dysmotility in SSc is poorly understood. To determine whether distinct changes in esophageal epithelial cells contribute to impaired motility in SSc, we investigated the stratified squamous esophageal epithelium using single-cell RNA sequencing (n=306,372 cells) in individuals with SSc compared those with gastroesophageal reflux disease (GERD) as well as healthy controls. The proportion of epithelial cells in the outermost, superficial compartment of the esophageal epithelium was significantly reduced in SSc (9.4% vs 21.6% in HCs). Differential gene expression in SSc was primarily limited to the superficial compartment (3,572 genes vs. 232 in all other compartments), with significant upregulation of extracellular matrix and keratinization genes. These cellular and molecular changes in SSc were highly correlated with those seen in GERD, indicating they were secondary to reflux; however, their magnitudes were more pronounced in the proximal esophagus, suggesting that esophageal dysmotility leads to greater proximal acid exposure, which may contribute to aspiration. SSc-specific gene dysregulation implicated immunoregulatory pathways likely pertinent to pathogenic mechanisms. By offering a comprehensive view of transcriptional dysregulation at single-cell resolution in human esophageal epithelial cells in SSc compared to GERD and healthy tissue, this work clarifies the state of epithelial cells in SSc-induced esophageal dysfunction.

Nothing to disclose: MD, MHC, HMM, TT, CW, MC, KA, MPT. DAC has received consulting or speaking fees from Medpace and Medtronic; LNM from American College of Surgeons; CLR from Cabaletta Bio; JP from Covidien, EndoGastric Solutions, HS Consolidated, Medtronic Logistics, Medtronic, Phathom Pharmaceuticals, UpToDate, WebMD; HP from American Society for Clinical Investigation, AnaptysBio, Arthritis Research & Therapy, General Dynamics Information Technology, and L.E.K. Consulting; DW from Gerson Lehrman Group. DAC and JEP have a licensing agreement with Medtronic.

This work was funded by NIH NIDDK P01DK117824 and the Digestive Health Foundation.

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The Institutional Review Board of Northwestern University gave ethical approval for this work.

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