Journal
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
Volume 8, Issue 3, Pages 407-426Publisher
ELSEVIER INC
DOI: 10.1016/j.jcmgh.2019.06.001
Keywords
Short Gut Syndrome; Enterocyte; Single-Cell RNA Sequencing; Creb3l3; Retinoid Metabolism
Categories
Funding
- Children's Discovery Institute of Washington University in St. Louis
- Children's Discovery Institute of St. Louis Children's Hospital [MI-II-2016-544, MI-F-2017-629, CDI-CORE-2015-505]
- National Institutes of Health [R01-GM126112, 5T32GM007067-44]
- Silicon Valley Community Foundation
- Chan Zuckerberg Initiative [HCA2-A-1708-02799]
- Washington University Digestive Diseases Research Core Center, National Institute of Diabetes and Digestive and Kidney Diseases [P30DK052574]
- Children's Surgical Sciences Research Institute of the St. Louis Children's Hospital
- Association for Academic Surgery Foundation
- Vallee Scholar Award
- Washington University School of Medicine
- Children's Discovery Institute of Washington University
- Foundation for Barnes-Jewish Hospital [3770]
- Washington University Digestive Diseases Research Core Center
- [4T32HD043010-14]
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BACKGROUND & AIMS: The small intestine (SI) displays regionality in nutrient and immunological function. Following SI tissue loss (as occurs in short gut syndrome, or SGS), remaining SI must compensate, or adapt; the capacity of SI epithelium to reprogram its regional identity has not been described. Here, we apply single-cell resolution analyses to characterize molecular changes underpinning adaptation to SGS. METHODS: Single-cell RNA sequencing was performed on epithelial cells isolated from distal SI of mice following 50% proximal small bowel resection (SBR) vs sham surgery. Single-cell profiles were clustered based on transcriptional similarity, reconstructing differentiation events from intestinal stem cells (ISCs) through to mature enterocytes. An unsupervised computational approach to score cell identity was used to quantify changes in regional (proximal vs distal) SI identity, validated using immunofluorescence, immunohistochemistry, qPCR, western blotting, and RNA-FISH. RESULTS: Uniform Manifold Approximation and Projection-based clustering and visualization revealed differentiation trajectories from ISCs to mature enterocytes in sham and SBR. Cell identity scoring demonstrated segregation of enterocytes by regional SI identity: SBR enterocytes assumed more mature proximal identities. This was associated with significant upregulation of lipid metabolism and oxidative stress gene expression, which was validated via orthogonal analyses. Observed upstream transcriptional changes suggest retinoid metabolism and proximal transcription factor Creb3l3 drive proximalization of cell identity in response to SBR. CONCLUSIONS: Adaptation to proximal SBR involves regional reprogramming of ileal enterocytes toward a proximal identity. Interventions bolstering the endogenous reprogramming capacity of SI enterocytes-conceivably by engaging the retinoid metabolism pathway-merit further investigation, as they may increase enteral feeding tolerance, and obviate intestinal failure, in SGS.
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