Single-Cell Analysis Reveals Regional Reprogramming During Adaptation to Massive Small Bowel Resection in Mice.
Animals
Cellular Reprogramming
Cyclic AMP Response Element-Binding Protein
/ genetics
Enterocytes
/ chemistry
Gene Expression Profiling
/ methods
Gene Regulatory Networks
Intestine, Small
/ chemistry
Lipid Metabolism
Male
Mice
Oxidative Stress
RNA, Small Nuclear
/ pharmacology
Sequence Analysis, RNA
/ methods
Single-Cell Analysis
/ methods
Unsupervised Machine Learning
Up-Regulation
Creb3l3
Enterocyte
Retinoid Metabolism
Short Gut Syndrome
Single-Cell RNA Sequencing
Journal
Cellular and molecular gastroenterology and hepatology
ISSN: 2352-345X
Titre abrégé: Cell Mol Gastroenterol Hepatol
Pays: United States
ID NLM: 101648302
Informations de publication
Date de publication:
2019
2019
Historique:
received:
16
08
2018
revised:
29
05
2019
accepted:
03
06
2019
pubmed:
14
6
2019
medline:
21
7
2020
entrez:
14
6
2019
Statut:
ppublish
Résumé
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. 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. 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. 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.
Sections du résumé
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.
Identifiants
pubmed: 31195149
pii: S2352-345X(19)30079-7
doi: 10.1016/j.jcmgh.2019.06.001
pmc: PMC6718927
pii:
doi:
Substances chimiques
Creb3l3 protein, mouse
0
Cyclic AMP Response Element-Binding Protein
0
RNA, Small Nuclear
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
407-426Subventions
Organisme : NIDDK NIH HHS
ID : P30 DK056341
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM126112
Pays : United States
Organisme : NICHD NIH HHS
ID : T32 HD043010
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007067
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK052574
Pays : United States
Informations de copyright
Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.
Références
Cell. 2018 Nov 1;175(4):1156-1167.e15
pubmed: 30270040
J Clin Invest. 2015 Jul 1;125(7):2646-60
pubmed: 26053663
Food Chem. 2015 Apr 1;172:155-60
pubmed: 25442537
J Pediatr Gastroenterol Nutr. 2017 Nov;65(5):588-596
pubmed: 28837507
Nature. 2008 Nov 20;456(7220):350-6
pubmed: 19043829
Surgery. 2017 Apr;161(4):1016-1027
pubmed: 28011012
J Surg Res. 2017 Dec;220:182-196
pubmed: 29180181
Am J Physiol Gastrointest Liver Physiol. 2007 Jun;292(6):G1559-69
pubmed: 17307727
BMC Genomics. 2015 Sep 03;16:676
pubmed: 26335021
Cell Mol Life Sci. 2017 Feb;74(4):607-616
pubmed: 27563706
Mol Vis. 2010 Apr 15;16:689-97
pubmed: 20405022
Am J Physiol Gastrointest Liver Physiol. 2011 May;300(5):G803-14
pubmed: 21350192
J Pediatr. 2001 Jul;139(1):27-33
pubmed: 11445790
Physiol Genomics. 2007 Jul 18;30(2):192-204
pubmed: 17426115
Biochem Pharmacol. 2008 Mar 1;75(5):1129-60
pubmed: 18164278
J Gastrointest Surg. 2014 Feb;18(2):286-94; discussion 294
pubmed: 24002772
J Pediatr Surg. 2013 Jun;48(6):1330-9
pubmed: 23845627
Sci Rep. 2014 Jul 04;4:5577
pubmed: 24993014
Bioinformatics. 2011 Apr 1;27(7):1017-8
pubmed: 21330290
Am J Physiol Heart Circ Physiol. 2016 Jun 1;310(11):H1773-89
pubmed: 27084391
Sci Rep. 2016 Dec 16;6:39182
pubmed: 27982131
Brain Res Mol Brain Res. 2002 Feb 28;99(1):34-9
pubmed: 11869806
Cancer Sci. 2015 May;106(5):567-75
pubmed: 25683251
Gastroenterology. 2005 Nov;129(5):1567-80
pubmed: 16285956
Prostaglandins Leukot Essent Fatty Acids. 2015 Feb;93:9-16
pubmed: 25458898
Gastroenterology. 1978 Aug;75(2):249-54
pubmed: 669211
J Pharmacol Exp Ther. 2000 Dec;295(3):979-85
pubmed: 11082432
Am J Physiol Gastrointest Liver Physiol. 2014 Mar;306(6):G474-90
pubmed: 24436352
J Pediatr. 2012 Oct;161(4):723-8.e2
pubmed: 22578586
Int J Mol Med. 2015 Mar;35(3):724-30
pubmed: 25585692
Cell Mol Gastroenterol Hepatol. 2016 Dec 10;3(2):231-244
pubmed: 28275690
PLoS One. 2012;7(9):e45725
pubmed: 23049847
Nat Rev Immunol. 2008 Sep;8(9):685-98
pubmed: 19172691
Syst Biol Reprod Med. 2009 Aug;55(4):145-63
pubmed: 19886770
Science. 1990 Oct 19;250(4979):399-404
pubmed: 2218545
Am J Anat. 1981 Jan;160(1):93-103
pubmed: 7211719
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Subcell Biochem. 2016;81:21-76
pubmed: 27830500
J Pediatr Surg. 2015 Jun;50(6):948-53
pubmed: 25818317
J Gastrointest Surg. 2008 Nov;12(11):1854-64; discussion 1864-5
pubmed: 18766411
Biochem Biophys Res Commun. 2002 May 10;293(3):913-7
pubmed: 12051745
Nature. 2016 Jun 08;534(7607):391-5
pubmed: 27281220
Adipocyte. 2016 Oct 10;5(4):378-383
pubmed: 27994952
Dev Biol. 2017 Apr 15;424(2):208-220
pubmed: 28274610
Neurosci Lett. 1997 Jan 17;221(2-3):73-6
pubmed: 9121703
Nat Biotechnol. 2018 Jun;36(5):411-420
pubmed: 29608179
Biochim Biophys Acta. 2012 Jan;1821(1):21-56
pubmed: 22020178
Nat Biotechnol. 2018 Dec 03;:
pubmed: 30531897
Hypertension. 2004 Dec;44(6):907-12
pubmed: 15477383
Nature. 2016 Jun 08;534(7606):191-9
pubmed: 27279212
BMC Biol. 2017 May 19;15(1):44
pubmed: 28526029
Biochem Biophys Res Commun. 2010 Jan 8;391(2):1222-7
pubmed: 20006574
J Lipid Res. 2002 Nov;43(11):1773-808
pubmed: 12401878
J Clin Invest. 1998 Aug 1;102(3):625-32
pubmed: 9691099
J Invest Dermatol. 1994 May;102(5):730-3
pubmed: 8176254
J Biol Chem. 2016 Sep 2;291(36):18991-9005
pubmed: 27402828
Am J Physiol Gastrointest Liver Physiol. 2009 May;296(5):G1108-18
pubmed: 19228882
Nature. 2018 Dec;564(7735):219-224
pubmed: 30518857
Am J Physiol Gastrointest Liver Physiol. 2017 Sep 1;313(3):G247-G255
pubmed: 28619728
J Biol Chem. 2012 Mar 30;287(14):10799-811
pubmed: 22337869
Am J Physiol Gastrointest Liver Physiol. 2003 Aug;285(2):G424-32
pubmed: 12711591
J Nutr. 1997 Jul;127(7):1297-303
pubmed: 9202083
J Pediatr Surg. 2005 Jan;40(1):92-7
pubmed: 15868565
Curr Biol. 2008 Mar 11;18(5):R191-2
pubmed: 18334189
J Am Coll Surg. 1996 Nov;183(5):441-9
pubmed: 8912612
BMC Cancer. 2014 Sep 23;14:693
pubmed: 25245097
Am J Physiol Renal Physiol. 2001 Nov;281(5):F909-19
pubmed: 11592949
Gut. 1987 Aug;28(8):981-7
pubmed: 2889650
Curr Gastroenterol Rep. 2015 Jan;17(1):427
pubmed: 25613179
Arch Biochem Biophys. 2014 Jan 1;541:30-6
pubmed: 24157689
Exp Cell Res. 2008 Dec 10;314(20):3712-23
pubmed: 18977346
Nat Med. 2014 Nov;20(11):1310-4
pubmed: 25326803
FEBS Lett. 1997 Aug 4;412(3):480-4
pubmed: 9276450
JPEN J Parenter Enteral Nutr. 2000 Mar-Apr;24(2):81-8
pubmed: 10772187
Am J Physiol Gastrointest Liver Physiol. 2002 Jun;282(6):G1079-87
pubmed: 12016134
Nature. 2017 Nov 16;551(7680):333-339
pubmed: 29144463
JPEN J Parenter Enteral Nutr. 2004 Nov-Dec;28(6):399-409
pubmed: 15568286
Nat Commun. 2017 Jan 16;8:14049
pubmed: 28091601
Gastroenterology. 2011 Jul;141(1):176-85
pubmed: 21596042
J Cell Sci. 2012 Apr 1;125(Pt 7):1827-36
pubmed: 22366455
Gastroenterology. 1976 May;70(5 PT.1):712-9
pubmed: 816699
Am J Physiol Gastrointest Liver Physiol. 2007 Jan;292(1):G215-22
pubmed: 16920699
Front Physiol. 2017 Feb 07;8:61
pubmed: 28223944
Sci Rep. 2016 Jun 28;6:28990
pubmed: 27350069
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W305-11
pubmed: 19465376
Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2613-8
pubmed: 11867749
Nat Biotechnol. 2015 May;33(5):495-502
pubmed: 25867923