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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 3

Differential gene expression between conditions in EECs.

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Differential gene expression between conditions in EECs.
(A) The number ...
(A) The number of significantly differentially expressed genes at the single-cell level (Wilcoxon’s rank-sum) with |log2 fold change| > 0.1 is shown for SSc versus HCs (purple) and GERD versus HCs (orange), by epithelial compartment and biopsy location. Blue bars account for genes that were differentially expressed in both SSc and GERD compared with HCs. (B) Gene set enrichment analysis results, showing all pathways enriched with P < 0.001 (unadjusted; 100,000 permutations) for SSc versus HCs (purple) and GERD versus HCs (orange), split by non-proliferating epithelial compartment and biopsy location. Points circled in red indicate statistical significance after adjustment for the number of tested pathways (PFDR < 0.05). (C) The distribution of intra-sample EEC gene expression correlations for the 2,000 most variable genes between proximal and distal biopsies is shown by epithelial compartment and condition. Box whiskers extend to range of values. (D) Pseudobulk gene expression differences in log2 fold change (log2FC) are shown for SSc versus HCs (y axis) against GERD versus HCs (x axis) within the superficial compartment in the proximal and distal esophagus regions. Significant DEGs in both conditions are highlighted in blue, significant DEGs in SSC only are highlighted in purple, and significant DEGs in GERD only are highlighted in orange (edgeR) (97). The correlation between comparisons is shown at upper left, and the slope and coefficient of determination for the modeled linear regression with intercept = 0 are displayed at lower right. Trendlines with 95% confidence intervals are plotted in pink, and dashed gray lines denote where y = x. Encircled points highlight disease-specific DEGs that are referenced in the main text and plotted in Supplemental Figure 5H, which shows the distribution of expression aggregated by sample in the superficial compartment across conditions and biopsy locations.

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