Single-Cell Analysis Reveals Regional Reprogramming During Adaptation to Massive Small Bowel Resection in Mice
| Autor: | Kenji Kamimoto, Samantha A. Morris, Brad W. Warner, Cathleen M. Courtney, Wenjun Kong, William H. Goo, Sarah E. Waye, Kristen M. Seiler, Adam Bajinting, Jun Guo, Emily J. Onufer |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Male SBR small bowel resection PBST phosphate-buffered saline + TWEEN 20 Single-Cell RNA Sequencing Mice 0302 clinical medicine Single-cell analysis RARE retinoic acid response element RNA Small Nuclear Gene expression Intestine Small RA retinoic acid Gene Regulatory Networks Cyclic AMP Response Element-Binding Protein ADA adenosine deaminase Original Research scRNA-seq single-cell RNA sequencing 0303 health sciences Short Gut Syndrome Gastroenterology SGS short gut syndrome Cellular Reprogramming PPRE peroxisome proliferator-activated receptor response element mRNA messenger RNA Cell biology Up-Regulation medicine.anatomical_structure 030220 oncology & carcinogenesis AU arbitrary units Enterocyte qPCR quantitative polymerase chain reaction 030211 gastroenterology & hepatology Stem cell Single-Cell Analysis Reprogramming Creb3l3 Retinoid Metabolism TOM Topological Overlap Matrix RNA-FISH RNA fluorescence in situ hybridization RXR retinoid X receptor PBS phosphate-buffered saline Biology 03 medical and health sciences cDNA complementary DNA PN parenteral nutrition SI small intestine Downregulation and upregulation medicine UMAP Uniform Manifold Approximation and Projection Animals lcsh:RC799-869 Transcription factor UMI unique molecular identifier 030304 developmental biology Hepatology PPARα peroxisome proliferator-activated receptor alpha Sequence Analysis RNA Gene Expression Profiling DGE digital gene expression TA transit amplifying Lipid Metabolism Epithelium Small intestine Oxidative Stress 030104 developmental biology Enterocytes RAR retinoic acid receptor QP quadratic programming lcsh:Diseases of the digestive system. Gastroenterology Unsupervised Machine Learning |
| Zdroj: | Cellular and Molecular Gastroenterology and Hepatology Cellular and Molecular Gastroenterology and Hepatology, Vol 8, Iss 3, Pp 407-426 (2019) |
| ISSN: | 2352-345X |
| Popis: | 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. Graphical abstract |
| Databáze: | OpenAIRE |
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