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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 4

Landscape of superficial EECs.

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Landscape of superficial EECs.
(A) Integrated UMAP embedding of all supe...
(A) Integrated UMAP embedding of all superficial EECs (n = 30,866) clustered by unique transcriptional signatures. (B) Relative expression of cluster-specific gene signatures. (C) Superficial module score by superficial cell cluster. (D) CosMx spatial molecular imaging of esophageal mucosal tissue from a healthy control donor and in SSc with absent contractility, annotated using label transfer from the scRNA-seq data. Superficial cluster proportions were derived from all imaged proximal tissue (n = 2 SSc, 2 HCs). (E) Proportion of superficial cells by condition and cluster from the proximal esophagus. The bars denote the mean values, the vertical lines the standard deviations, and the points the individual sample proportions. Pairwise differences across conditions were evaluated statistically using MASC (96). *P < 0.05. (F) Distribution of metallothionein module score in proximal, superficial cells by condition. The metallothionein module score included MT1A, MT1E, MT1F, MT1G, MT1H, MT1M, MT1X, and MT2A. (G) Distribution of relative metallothionein expression by cluster and condition in superficial cells from proximal esophagus. All pairwise comparisons between SSc and HCs were statistically significant, except for cluster 5. (H) CosMx spatial molecular imaging of esophageal mucosal tissue from a healthy control donor and in scleroderma with absent contractility. Metallothionein module scores are plotted within the superficial EECs. (I) Distributions of metallothionein module scores by cell cluster and condition from the CosMx spatial molecular imaging data. Significant pairwise differences (Wilcoxon’s rank-sum) in module score levels (PFDR < 0.05) are denoted with an asterisk.

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