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Cellular and molecular dysregulation of the esophageal epithelium in systemic sclerosis
Matthew Dapas, Margarette H. Clevenger, Hadijat-Kubura M. Makinde, Tyler Therron, Dustin A. Carlson, Mary Carns, Kathleen Aren, Cenfu Wei, Kainat Mian, Lutfiyya N. Muhammad, Carrie Richardson, Parambir S. Dulai, Monique Hinchcliff, John Pandolfino, Harris Perlman, Deborah R. Winter, Marie-Pier Tetreault
Matthew Dapas, Margarette H. Clevenger, Hadijat-Kubura M. Makinde, Tyler Therron, Dustin A. Carlson, Mary Carns, Kathleen Aren, Cenfu Wei, Kainat Mian, Lutfiyya N. Muhammad, Carrie Richardson, Parambir S. Dulai, Monique Hinchcliff, John Pandolfino, Harris Perlman, Deborah R. Winter, Marie-Pier Tetreault
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Research Article Gastroenterology Immunology

Cellular and molecular dysregulation of the esophageal epithelium in systemic sclerosis

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Abstract

Systemic sclerosis (SSc) is a rare autoimmune disease characterized by vasculopathy and fibrosis of the skin and internal organs. Individuals with SSc often suffer from chronic acid reflux and dysphagia due to loss of esophageal motility. To determine whether distinct changes in esophageal epithelial cells contribute to esophageal involvement in SSc, we investigated the stratified squamous esophageal epithelium from proximal and distal biopsies using single-cell RNA sequencing in individuals with SSc compared with those with gastroesophageal reflux disease (GERD) and healthy controls. 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. Ligand-receptor interaction analysis revealed enhanced profibrotic signaling between fibroblasts and epithelial cells in SSc. Cell type localization and SSc-specific changes were confirmed by spatial molecular imaging. By offering a comprehensive view of transcriptional dysregulation at single-cell resolution in human esophageal epithelial cells in SSc compared with GERD and healthy tissue, this work clarifies the state of epithelial cells in SSc-induced esophageal dysfunction.

Authors

Matthew Dapas, Margarette H. Clevenger, Hadijat-Kubura M. Makinde, Tyler Therron, Dustin A. Carlson, Mary Carns, Kathleen Aren, Cenfu Wei, Kainat Mian, Lutfiyya N. Muhammad, Carrie Richardson, Parambir S. Dulai, Monique Hinchcliff, John Pandolfino, Harris Perlman, Deborah R. Winter, Marie-Pier Tetreault

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Figure 5

Intercellular interactions and spatial proximity.

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Intercellular interactions and spatial proximity.
(A) Heatmap of differe...
(A) Heatmap of differential interaction strength between SSc and combined GERD and HCs. Rows indicate source (sender) cell types, and columns indicate target (receiver) cell types. Color intensity reflects relative increase (red) or decrease (blue) in interaction strength in SSc. Marginal bar plots show aggregate differential signaling strength per cell type as senders (rows) or receivers (columns). (B) Differential signaling roles across pairwise condition comparisons. Each point represents a cell type, with x axis and y axis indicating differential outgoing and incoming interaction strength, respectively. Positive values indicate increased signaling in the first condition of each comparison. (C) Relative contribution of cell types to incoming (left) and outgoing (right) signaling for pathways with significant differential activity in SSc. Heatmap values are row-scaled. Gray bars indicate aggregate signaling strength per pathway summed across all cell types. Top colored bars indicate aggregate signaling strength per cell type summed across displayed pathways. (D) Spatial neighborhood composition of epithelial subtypes from CosMx spatial molecular imaging data. Top: Proportion of non-epithelial neighbors by cell type for each epithelial subtype in HC and SSc. Bottom: Relative composition of non-epithelial neighbors. (E) Change in the proportion of epithelial cell neighbors by non-epithelial cell type between SSc and HCs. (F) Cell type composition of fibroblast spatial neighbors in HCs and SSc.

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