Single-cell RNA-Seq of human esophageal epithelium in homeostasis and allergic inflammation
Mark Rochman, Ting Wen, Michael Kotliar, Phillip J. Dexheimer, Netali Ben-Baruch Morgenstern, Julie M. Caldwell, Hee-Woong Lim, Marc E. Rothenberg
Mark Rochman, Ting Wen, Michael Kotliar, Phillip J. Dexheimer, Netali Ben-Baruch Morgenstern, Julie M. Caldwell, Hee-Woong Lim, Marc E. Rothenberg
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Research Article Immunology Inflammation

Single-cell RNA-Seq of human esophageal epithelium in homeostasis and allergic inflammation

Abstract

Inflammation of the esophageal epithelium is a hallmark of eosinophilic esophagitis (EoE), an emerging chronic allergic disease. Herein, we probed human esophageal epithelial cells at single-cell resolution during homeostasis and EoE. During allergic inflammation, the epithelial differentiation program was blocked, leading to loss of KRT6hi differentiated populations and expansion of TOP2hi proliferating, DSPhi transitioning, and SERPINB3hi transitioning populations; however, there was stability of the stem cell–enriched PDPNhi basal epithelial compartment. This differentiation program blockade was associated with dysregulation of transcription factors, including nuclear receptor signalers, in the most differentiated epithelial cells and altered NOTCH-related cell-to-cell communication. Each epithelial population expressed genes with allergic disease risk variants, supporting their functional interplay. The esophageal epithelium differed notably between EoE in histologic remission and controls, indicating that remission is a transitory state poised to relapse. Collectively, our data uncover the dynamic nature of the inflamed human esophageal epithelium and provide a framework to better understand esophageal health and disease.

Authors

Mark Rochman, Ting Wen, Michael Kotliar, Phillip J. Dexheimer, Netali Ben-Baruch Morgenstern, Julie M. Caldwell, Hee-Woong Lim, Marc E. Rothenberg

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Figure 6

Expression of transcription factors and NOTCH-related genes in human esophageal epithelial cells.

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Expression of transcription factors and NOTCH-related genes in human eso...
(A) Gene expression heatmap of subpopulation-specific transcription factors (TF) in the healthy control esophagus (Normal). (B) Log2FC of the subpopulation-specific TFs in the active EoE (Active) and remission EoE (Remiss) esophagus compared with the normal esophagus by pseudo-bulk RNA-Seq differential analysis (#FDR-adjusted P < 0.05). Genes are ordered the same as in B. (C) Gene expression heatmap of the NOTCH signaling pathway genes (KEGG) in the normal epithelial subpopulations. (D) Log2FC of the NOTCH gene expression in the active EoE (Active) and remission EoE (Remiss) esophagus compared with the normal esophagus by pseudo-bulk RNA-Seq differential analysis (#FDR-adjusted P < 0.05). Genes are ordered the same as in C. For B and D, Differentiatedhi and Differentiatedlo cell subpopulations are represented by 1 unified cell population. (E) Transepithelial electrical resistance (TEER) was measured in the EPC2 cells grown at the air-liquid interface (ALI) and treated as indicated. Data are from 3–5 independent experiments performed in triplicate. Data are shown as mean ± SEM. ****P < 0.0001 for ALI day 5 (D5) compared with untreated (UT), by 1-way ANOVA. Insets show representative H&E staining of the ALI cultures (×10 magnification). (F) Relative expression of involucrin in the EPC2 cells grown at the ALI for 5 days (ALI D5). Expression was normalized to GAPDH. Combined data for 3 independent cultures performed in duplicates is shown; data are shown as mean ± SEM. ****P < 0.0001 compared with UT, by 1-way ANOVA.