Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle content marks basal cells with limited proliferation and enhanced self-renewal potential

Klochkova, A.; Karami, A. L.; Fuller, A. D.; Parham, L. R.; Panchani, S. R.; Natarajan, S.; Jackson, J. L.; Mu, A.; Tan, Y.; Cai, K. Q.; Klein-Szanto, A.; Muir, A. B.; Tetreault, M.-P.; Hamilton, K. E.; Whelan, K. A.

doi:10.1101/2023.09.20.558614

bioRxiv · 10.1101/2023.09.20.558614

Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle content marks basal cells with limited proliferation and enhanced self-renewal potential

Klochkova, A.·Karami, A. L.·Fuller, A. D.·Parham, L. R.·Panchani, S. R.·Natarajan, S.·Jackson, J. L.·Mu, A.·Tan, Y.·Cai, K. Q.·Klein-Szanto, A.·Muir, A. B.·Tetreault, M.-P.·Hamilton, K. E.·Whelan, K. A.

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Abstract

Background & AimsAutophagy has been demonstrated to play roles in esophageal pathologies both benign and malignant. Here, we aim to define the role of autophagy in esophageal epithelium under homeostatic conditions. MethodsWe generated tamoxifen-inducible, squamous epithelial-specific Atg7 (autophagy related 7) conditional knockout mice to evaluate effects on esophageal homeostasis and response to the carcinogen 4-nitroquinoline 1-oxide (4NQO) using histological and biochemical analyses. We FACS sorted esophageal basal cells based upon fluorescence of the autophagic vesicle (AV)-identifying dye Cyto-ID, then subjected these cells to transmission electron microscopy, image flow cytometry, 3D organoid assays, RNA-Sequencing (RNA-Seq), and cell cycle analysis. 3D organoids were subjected to passaging, single cell (sc) RNA-Seq, cell cycle analysis, and immunostaining. ResultsGenetic autophagy inhibition in squamous epithelium resulted in increased proliferation of esophageal basal cells. Esophageal basal cells with high AV level (Cyto-IDHigh) displayed limited organoid formation capability upon initial plating but passaged more efficiently than their counterparts with low AV level (Cyto-IDLow). RNA-Seq suggested increased autophagy in Cyto- IDHigh esophageal basal cells along with decreased cell cycle progression, the latter of which was confirmed by cell cycle analysis. scRNA-Seq of 3D organoids generated by Cyto-IDLow and Cyto- IDHigh cells identified expansion of 3 cell populations, enrichment of G2/M-associated genes, and aberrant localization of cell cycle-associated genes beyond basal cell populations in the Cyto- IDHigh group. Ki67 expression was also increased in organoids generated by Cyto-IDHigh cells, including in cells beyond the basal cell layer. Squamous epithelial-specific autophagy inhibition induced significant weight loss in mice treated with 4NQO that further displayed perturbed epithelial tissue architecture. ConclusionsHigh AV level identifies esophageal epithelium with limited proliferation and enhanced self-renewal capacity that contributes to maintenance of the esophageal proliferation- differentiation gradient in vivo.

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Klochkova, A., Karami, A. L., Fuller, A. D., Parham, L. R., Panchani, S. R., Natarajan, S., Jackson, J. L., Mu, A., Tan, Y., Cai, K. Q., Klein-Szanto, A., Muir, A. B., Tetreault, M.-P., Hamilton, K. E., Whelan, K. A.. 2023-09-22. Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle content marks basal cells with limited proliferation and enhanced self-renewal potential. https://doi.org/10.1101/2023.09.20.558614

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