|
1
|
Yang X, Guo H and Zou M: Inflammatory
bowel diseases: Pathological mechanisms and therapeutic
perspectives. Mol Biomed. 7:22026. View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Piovani D, Danese S, Peyrin-Biroulet L,
Nikolopoulos GK, Lytras T and Bonovas S: Environmental Risk factors
for inflammatory bowel diseases: An umbrella review of
meta-analyses. Gastroenterology. 157:647–659.e4. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Estevinho MM, Midya V, Cohen-Mekelburg S,
Allin KH, Fumery M, Pinho SS, Colombel JF and Agrawal M: Emerging
role of environmental pollutants in inflammatory bowel disease
risk, outcomes and underlying mechanisms. Gut. 74:477–486. 2025.
View Article : Google Scholar
|
|
4
|
Shah SC and Itzkowitz SH: Colorectal
cancer in inflammatory bowel disease: Mechanisms and management.
Gastroenterology. 162:715–730.e3. 2022. View Article : Google Scholar
|
|
5
|
Iliev ID, Ananthakrishnan AN and Guo CJ:
Microbiota in inflammatory bowel disease: Mechanisms of disease and
therapeutic opportunities. Nat Rev Microbiol. 23:509–524. 2025.
View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Danne C, Skerniskyte J, Marteyn B and
Sokol H: Neutrophils: From IBD to the gut microbiota. Nat Rev
Gastroenterol Hepatol. 21:184–197. 2024. View Article : Google Scholar
|
|
7
|
Foerster EG, Mukherjee T, Cabral-Fernandes
L, Rocha JDB, Girardin SE and Philpott DJ: How autophagy controls
the intestinal epithelial barrier. Autophagy. 18:86–103. 2022.
View Article : Google Scholar :
|
|
8
|
Chen Y, Cui W, Li X and Yang H:
Interaction between commensal bacteria, immune response and the
intestinal barrier in inflammatory bowel disease. Front Immunol.
12:7619812021. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Dong L, Xie J, Wang Y, Jiang H, Chen K, Li
D, Wang J, Liu Y, He J, Zhou J, et al: Mannose ameliorates
experimental colitis by protecting intestinal barrier integrity.
Nat Commun. 13:48042022. View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Won TH, Arifuzzaman M, Parkhurst CN,
Miranda IC, Zhang B, Hu E, Kashyap S, Letourneau J, Jin WB, Fu Y,
et al: Host metabolism balances microbial regulation of bile acid
signalling. Nature. 638:216–224. 2025. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Chen L, Jiao T, Liu W, Luo Y, Wang J, Guo
X, Tong X, Lin Z, Sun C, Wang K, et al: Hepatic cytochrome P450 8B1
and cholic acid potentiate intestinal epithelial injury in colitis
by suppressing intestinal stem cell renewal. Cell Stem Cell.
29:1366–1381.e9. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Ding L, Yang L, Wang Z and Huang W: Bile
acid nuclear receptor FXR and digestive system diseases. Acta Pharm
Sin B. 5:135–144. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Li T, Ding N, Guo H, Hua R, Lin Z, Tian H,
Yu Y, Fan D, Yuan Z, Gonzalez FJ and Wu Y: A gut microbiota-bile
acid axis promotes intestinal homeostasis upon aspirin-mediated
damage. Cell Host Microbe. 32:191–208.e9. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Liu F, Yao Y, Wang Q, Zhang F, Wang M, Zhu
C and Lin C: Nigakinone alleviates DSS-induced experimental colitis
via regulating bile acid profile and FXR/NLRP3 signaling pathways.
Phytother Res. 37:15–34. 2023. View
Article : Google Scholar
|
|
15
|
Hou Q, Ye L, Liu H, Huang L, Yang Q,
Turner JR and Yu Q: Lactobacillus accelerates ISCs regeneration to
protect the integrity of intestinal mucosa through activation of
STAT3 signaling pathway induced by LPLs secretion of IL-22. Cell
Death Differ. 25:1657–1670. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Montgomery RK and Shivdasani RA: Prominin1
(CD133) as an intestinal stem cell marker: Promise and nuance.
Gastroenterology. 136:2051–2054. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Bao W, You Y, Ni J, Hou H, Lyu J, Feng G,
Wang Y, You K, Zhang S, Zhang L, et al: Inhibiting sorting nexin 10
promotes mucosal healing through SREBP2-mediated stemness
restoration of intestinal stem cells. Sci Adv. 9:eadh50162023.
View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Yuan SN, Wang MX, Han JL, Feng CY, Wang M,
Wang M, Sun JY, Li NY, Simal-Gandara J and Liu C: Improved colonic
inflammation by nervonic acid via inhibition of NF-κB signaling
pathway of DSS-induced colitis mice. Phytomedicine. 112:1547022023.
View Article : Google Scholar
|
|
19
|
Zheng J, Zhang J, Zhou Y, Zhang D, Guo H,
Li B and Cui S: Taurine alleviates experimental colitis by
enhancing intestinal barrier function and inhibiting inflammatory
response through TLR4/NF-κB signaling. J Agric Food Chem.
72:12119–12129. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Fujii Y, Yoshihashi K, Suzuki H, Tsutsumi
S, Mutoh H, Maeda S, Yamagata Y, Seto Y, Aburatani H and Hatakeyama
M: CDX1 confers intestinal phenotype on gastric epithelial cells
via induction of stemness-associated reprogramming factors SALL4
and KLF5. Proc Natl Acad Sci USA. 109:20584–20589. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Wang MQ, Zhang KH, Liu FL, Zhou R, Zeng Y,
Chen AL, Yu Y, Xia Q, Zhu CC and Lin CZ: Wedelolactone alleviates
cholestatic liver injury by regulating FXR-bile acid-NF-κB/NRF2
axis to reduce bile acid accumulation and its subsequent
inflammation and oxidative stress. Phytomedicine. 122:1551242024.
View Article : Google Scholar
|
|
22
|
Parikh K, Antanaviciute A, Fawkner-Corbett
D, Jagielowicz M, Aulicino A, Lagerholm C, Davis S, Kinchen J, Chen
HH, Alham NK, et al: Colonic epithelial cell diversity in health
and inflammatory bowel disease. Nature. 567:49–55. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Tran HTN, Ang KS, Chevrier M, Zhang X, Lee
NYS, Goh M and Chen J: A benchmark of batch-effect correction
methods for single-cell RNA sequencing data. Genome Biol.
21:122020. View Article : Google Scholar : PubMed/NCBI
|
|
24
|
Vancamelbeke M, Vanuytsel T, Farré R,
Verstockt S, Ferrante M, Van Assche G, Rutgeerts P, Schuit F,
Vermeire S, Arijs I and Cleynen I: Genetic and transcriptomic bases
of intestinal epithelial barrier dysfunction in inflammatory bowel
disease. Inflamm Bowel Dis. 23:1718–1729. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Bjerrum JT, Hansen M, Olsen J and Nielsen
OH: Genome-wide gene expression analysis of mucosal colonic
biopsies and isolated colonocytes suggests a continuous
inflammatory state in the lamina propria of patients with quiescent
ulcerative colitis. Inflamm Bowel Dis. 16:999–1007. 2010.
View Article : Google Scholar
|
|
26
|
Li K, Strauss R, Ouahed J, Chan D, Telesco
S, Shouval DS, Canavan JB, Brodmerkel C, Snapper SB and Friedman
JR: Molecular comparison of adult and pediatric ulcerative colitis
indicates broad similarity of molecular pathways in disease tissue.
J Pediatr Gastroenterol Nutr. 67:45–52. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Robinson MD, McCarthy DJ and Smyth GK:
edgeR: A BIoconductor package for differential expression analysis
of digital gene expression data. Bioinformatics. 26:139–140. 2010.
View Article : Google Scholar
|
|
28
|
Love MI, Huber W and Anders S: Moderated
estimation of fold change and dispersion for RNA-seq data with
DESeq2. Genome Biol. 15:5502014. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Liu S, Wang Z, Zhu R, Wang F, Cheng Y and
Liu Y: Three differential expression analysis methods for RNA
sequencing: Limma, EdgeR, DESeq2. J Vis Exp. 2021.
|
|
30
|
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW,
Shi W and Smyth GK: Limma powers differential expression analyses
for RNA-sequencing and microarray studies. Nucleic Acids Res.
43:e472015. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Langfelder P and Horvath S: WGCNA: An R
package for weighted correlation network analysis. BMC
Bioinformatics. 9:5592008. View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Zhu L, Gibson P, Currle DS, Tong Y,
Richardson RJ, Bayazitov IT, Poppleton H, Zakharenko S, Ellison DW
and Gilbertson RJ: Prominin 1 marks intestinal stem cells that are
susceptible to neoplastic transformation. Nature. 457:603–607.
2009. View Article : Google Scholar :
|
|
33
|
Barker N, van Es JH, Kuipers J, Kujala P,
van den Born M, Cozijnsen M, Haegebarth A, Korving J, Begthel H,
Peters PJ and Clevers H: Identification of stem cells in small
intestine and colon by marker gene Lgr5. Nature. 449:1003–1007.
2007. View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Liu T, Zhang L, Joo D and Sun SC: NF-κB
signaling in inflammation. Signal Transduct Target Ther.
2:170232017. View Article : Google Scholar
|
|
35
|
Rai A, Kapoor S, Singh S, Chatterji BP and
Panda D: Transcription factor NF-κB associates with microtubules
and stimulates apoptosis in response to suppression of microtubule
dynamics in MCF-7 cells. Biochem Pharmacol. 93:277–289. 2015.
View Article : Google Scholar
|
|
36
|
Yui S, Azzolin L, Maimets M, Pedersen MT,
Fordham RP, Hansen SL, Larsen HL, Guiu J, Alves MRP, Rundsten CF,
et al: YAP/TAZ-dependent reprogramming of colonic epithelium links
ECM remodeling to tissue regeneration. Cell Stem Cell. 22:35–49.e7.
2018. View Article : Google Scholar :
|
|
37
|
Zeuner A, Todaro M, Stassi G and De Maria
R: Colorectal cancer stem cells: From the crypt to the clinic. Cell
Stem Cell. 15:692–705. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Chen WD, Wang YD, Zhang L, Shiah S, Wang
M, Yang F, Yu D, Forman BM and Huang W: Farnesoid X receptor
alleviates age-related proliferation defects in regenerating mouse
livers by activating forkhead box m1b transcription. Hepatology.
51:953–962. 2010. View Article : Google Scholar
|
|
39
|
Seitz CS, Lin Q, Deng H and Khavari PA:
Alterations in NF-kappaB function in transgenic epithelial tissue
demonstrate a growth inhibitory role for NF-kappaB. Proc Natl Acad
Sci USA. 95:2307–2312. 1998. View Article : Google Scholar : PubMed/NCBI
|
|
40
|
Biton M, Haber AL, Rogel N, Burgin G,
Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, et
al: T helper cell cytokines modulate intestinal stem cell renewal
and differentiation. Cell. 175:1307–1320.e22. 2018. View Article : Google Scholar : PubMed/NCBI
|
