|
1
|
Podolsky DK: Inflammatory bowel disease. N
Engl J Med. 347:417–429. 2002. View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Ordas I, Eckmann L, Talamini M, Baumgart
DC and Sandborn WJ: Ulcerative colitis. Lancet. 380:1606–1619.
2012. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Jess T, Loftus EV Jr, Velayos FS, Harmsen
WS, Zinsmeister AR, Smyrk TC, Schleck CD, Tremaine WJ, Melton LJ
III, Munkholm P and Sandborn WJ: Risk of intestinal cancer in
inflammatory bowel disease: A population-based study from olmsted
county, Minnesota. Gastroenterology. 130:1039–1046. 2006.
View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Colombel JF, Narula N and Peyrin-Biroulet
L: Management strategies to improve outcomes of patients with
inflammatory bowel diseases. Gastroenterology. 152:351–361.e5.
2017. View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Venema WT Uniken, Voskuil MD, Dijkstra G,
Weersma RK and Festen EA: The genetic background of inflammatory
bowel disease: From correlation to causality. J Pathol.
241:146–158. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Sivanesan D, Beauchamp C, Quinou C, Lee J,
Lesage S, Chemtob S, Rioux JD and Michnick SW: IL23R (interleukin
23 receptor) variants protective against inflammatory bowel
diseases (IBD) display loss of function due to impaired protein
stability and intracellular trafficking. J Biol Chem.
291:8673–8685. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Alipour M, Zaidi D, Valcheva R, Jovel J,
Martínez I, Sergi C, Walter J, Mason AL, Wong GK, Dieleman LA, et
al: Mucosal barrier depletion and loss of bacterial diversity are
primary abnormalities in paediatric ulcerative colitis. J Crohns
Colitis. 10:462–471. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
8
|
Spisni E, Valerii MC, De Fazio L, Cavazza
E, Borsetti F, Sgromo A, Candela M, Centanni M, Rizello F and
Strillacci A: Cyclooxygenase-2 silencing for the treatment of
colitis: A combined in vivo strategy based on RNA interference and
engineered Escherichia coli. Mol Ther. 23:278–289. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Ostvik AE, Granlund AV, Bugge M, Nilsen
NJ, Torp SH, Waldum HL, Damås JK, Espevik T and Sandvik AK:
Enhanced expression of CXCL10 in inflammatory bowel disease:
Potential role of mucosal Toll-like receptor 3 stimulation. Inflamm
Bowel Dis. 19:265–274. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Burczynski ME, Peterson RL, Twine NC,
Zuberek KA, Brodeur BJ, Casciotti L, Maganti V, Reddy PS, Strahs A,
Immermann F, et al: Molecular classification of Crohn's disease and
ulcerative colitis patients using transcriptional profiles in
peripheral blood mononuclear cells. J Mol Diagn. 8:51–61. 2006.
View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Montero-Meléndez T, Llor X,
Garcia-Planella E, Perretti M and Suárez A: Identification of novel
predictor classifiers for inflammatory bowel disease by gene
expression profiling. PLoS One. 8:e762352013. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Pekow J, Dougherty U, Huang Y, Gometz E,
Nathanson J, Cohen G, Levy S, Kocherginsky M, Venu N, Westerhoff M,
et al: Gene signature distinguishes patients with chronic
ulcerative colitis harboring remote neoplastic lesions. Inflamm
Bowel Dis. 19:461–470. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Planell N, Lozano JJ, Mora-Buch R,
Masamunt MC, Jimeno M, Ordás I, Esteller M, Ricart E, Piqué JM,
Panés J and Salas A: Transcriptional analysis of the intestinal
mucosa of patients with ulcerative colitis in remission reveals
lasting epithelial cell alterations. Gut. 62:967–976. 2013.
View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Bjerrum JT, Nielsen OH, Riis LB, Pittet V,
Mueller C, Rogler G and Olsen J: Transcriptional analysis of
left-sided colitis, pancolitis, and ulcerative colitis-associated
dysplasia. Inflamm Bowel Dis. 20:2340–2352. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
15
|
Smith PJ, Levine AP, Dunne J, Guilhamon P,
Turmaine M, Sewell GW, O'Shea NR, Vega R, Paterson JC, Oukrif D, et
al: Mucosal transcriptomics implicates under expression of BRINP3
in the pathogenesis of ulcerative colitis. Inflamm Bowel Dis.
20:1802–1812. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
van der Goten J, Vanhove W, Lemaire K, Van
Lommel L, Machiels K, Wollants WJ, De Preter V, De Hertogh G,
Ferrante M, Van Assche G, et al: Integrated miRNA and mRNA
expression profiling in inflamed colon of patients with ulcerative
colitis. PLoS One. 9:e1161172014. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Vanhove W, Peeters PM, Staelens D,
Schraenen A, Van Der Goten J, Cleynen I, De Schepper S, Van Lommel
L, Reynaert NL, Schuit F, et al: Strong upregulation of AIM2 and
IFI16 inflammasomes in the Mucosa of patients with active
inflammatory bowel disease. Inflamm Bowel Dis. 21:2673–2682. 2015.
View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Wu F, Dassopoulos T, Cope L, Maitra A,
Brant SR, Harris ML, Bayless TM, Parmigiani G and Chakravarti S:
Genome-wide gene expression differences in Crohn's disease and
ulcerative colitis from endoscopic pinch biopsies: Insights into
distinctive pathogenesis. Inflamm Bowel Dis. 13:807–821. 2007.
View Article : Google Scholar : PubMed/NCBI
|
|
19
|
Gurram B, Salzman NH, Kaldunski ML, Jia S,
Li BU, Stephens M, Sood MR and Hessner MJ: Plasma-induced
signatures reveal an extracellular milieu possessing an
immunoregulatory bias in treatment-naive paediatric inflammatory
bowel disease. Clin Exp Immunol. 184:36–49. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Olsen J, Gerds TA, Seidelin JB, Csillag C,
Bjerrum JT, Troelsen JT and Nielsen OH: Diagnosis of ulcerative
colitis before onset of inflammation by multivariate modeling of
genome-wide gene expression data. Inflamm Bowel Dis. 15:1032–1038.
2009. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
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
|
|
22
|
da W Huang, Sherman BT and Lempicki RA:
Bioinformatics enrichment tools: Paths toward the comprehensive
functional analysis of large gene lists. Nucleic Acids Res.
37:1–13. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Szklarczyk D, Franceschini A, Wyder S,
Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos
A, Tsafou KP, et al: STRING v10: Protein-protein interaction
networks, integrated over the tree of life. Nucleic Acids Res.
43(Database issue): D447–D452. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
24
|
von Mering C, Jensen LJ, Snel B, Hooper
SD, Krupp M, Foglierini M, Jouffre N, Huynen MA and Bork P: STRING:
Known and predicted protein-protein associations, integrated and
transferred across organisms. Nucleic Acids Res. 33(Database
issue): D433–D437. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Shannon P, Markiel A, Ozier O, Baliga NS,
Wang JT, Ramage D, Amin N, Schwikowski B and Ideker T: Cytoscape: A
software environment for integrated models of biomolecular
interaction networks. Genome Res. 13:2498–2504. 2003. View Article : Google Scholar : PubMed/NCBI
|
|
26
|
Wang J, Duncan D, Shi Z and Zhang B:
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): Update 2013.
Nucleic Acids Res. 41:W77–W83. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Li Y, Deuring J, Peppelenbosch MP, Kuipers
EJ, de Haar C and van der Woude CJ: STAT1, STAT6 and adenosine
3′,5′-cyclic monophosphate (cAMP) signaling drive SOCS3 expression
in inactive ulcerative colitis. Mol Med. 18:1412–1419. 2012.
View Article : Google Scholar : PubMed/NCBI
|
|
28
|
Christophi GP, Rong R, Holtzapple PG,
Massa PT and Landas SK: Immune markers and differential signaling
networks in ulcerative colitis and Crohn's disease. Inflamm Bowel
Dis. 18:2342–2356. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Holgersen K, Kutlu B, Fox B, Serikawa K,
Lord J, Hansen AK and Holm TL: High-resolution gene expression
profiling using RNA sequencing in patients with inflammatory bowel
disease and in mouse models of colitis. J Crohn's Colitis.
9:492–506. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Harris RA, Nagy-Szakal D, Mir SA, Frank E,
Szigeti R, Kaplan JL, Bronsky J, Opekun A, Ferry GD, Winter H, et
al: DNA methylation-associated colonic mucosal immune and defense
responses in treatment-naïve pediatric ulcerative colitis.
Epigenetics. 9:1131–1137. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Shiotani A, Kusunoki H, Kimura Y, Ishii M,
Imamura H, Tarumi K, Manabe N, Kamada T, Hata J and Haruma K: S100A
expression and interleukin-10 polymorphisms are associated with
ulcerative colitis and diarrhea predominant irritable bowel
syndrome. Dig Dis Sci. 58:2314–2323. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Miao YL, Xiao YL, Du Y and Duan LP: Gene
expression profiles in peripheral blood mononuclear cells of
ulcerative colitis patients. World J Gastroenterol. 19:3339–3346.
2013. View Article : Google Scholar : PubMed/NCBI
|
|
33
|
Deng X, Tolstanova G, Khomenko T, Chen L,
Tarnawski A, Szabo S and Sandor Z: Mesalamine restores angiogenic
balance in experimental ulcerative colitis by reducing expression
of endostatin and angiostatin: Novel molecular mechanism for
therapeutic action of mesalamine. J Pharmacol Exp Ther.
331:1071–1078. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Vong L, Ferraz JG, Dufton N, Panaccione R,
Beck PL, Sherman PM, Perretti M and Wallace JL: Up-regulation of
Annexin-A1 and lipoxin A(4) in individuals with ulcerative colitis
may promote mucosal homeostasis. PLoS One. 7:e392442012. View Article : Google Scholar : PubMed/NCBI
|
|
35
|
Sena AA, Pedrotti LP, Barrios BE, Cejas H,
Balderramo D, Diller A and Correa SG: Lack of TNFRI signaling
enhances annexin A1 biological activity in intestinal inflammation.
Biochem Pharmacol. 98:422–431. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Babbin BA, Lee WY, Parkos CA, Winfree LM,
Akyildiz A, Perretti M and Nusrat A: Annexin I regulates SKCO-15
cell invasion by signaling through formyl peptide receptors. J Biol
Chem. 281:19588–19599. 2006. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Leoni G, Alam A, Neumann PA, Lambeth JD,
Cheng G, McCoy J, Hilgarth RS, Kundu K, Murthy N, Kusters D, et al:
Annexin A1, formyl peptide receptor, and NOX1 orchestrate
epithelial repair. J Clin Invest. 123:443–454. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Xu AT, Li Y, Zhao D, Shen J, Xu XT, Qiao
YQ, Zhu MM, Wang TR, Cui Y, Ai LY, et al: High suppressor of
cytokine signaling-3 expression impairs STAT3-dependent protective
effects of interleukin-22 in ulcerative colitis in remission.
Inflamm Bowel Dis. 21:241–250. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
39
|
Fang K, Grisham MB and Kevil CG:
Application of comparative transcriptional genomics to identify
molecular targets for pediatric IBD. Front Immunol. 6:1652015.
View Article : Google Scholar : PubMed/NCBI
|
|
40
|
Mesko B, Poliska S, Szegedi A, Szekanecz
Z, Palatka K, Papp M and Nagy L: Peripheral blood gene expression
patterns discriminate among chronic inflammatory diseases and
healthy controls and identify novel targets. BMC Med Genomics.
3:152010. View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Huang Y and Chen Z: Inflammatory bowel
disease related innate immunity and adaptive immunity. Am J Transl
Res. 8:2490–2497. 2016.PubMed/NCBI
|
|
42
|
Murano T, Okamoto R, Ito G, Nakata T,
Hibiya S, Shimizu H, Fujii S, Kano Y, Mizutani T, Yui S, et al:
Hes1 promotes the IL-22-mediated antimicrobial response by
enhancing STAT3-dependent transcription in human intestinal
epithelial cells. Biochem Biophys Res Commun. 443:840–846. 2014.
View Article : Google Scholar : PubMed/NCBI
|
|
43
|
Clavel T and Haller D: Bacteria- and
host-derived mechanisms to control intestinal epithelial cell
homeostasis: Implications for chronic inflammation. Inflamm Bowel
Dis. 13:1153–1164. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
44
|
Yadav V, Varum F, Bravo R, Furrer E, Bojic
D and Basit AW: Inflammatory bowel disease: Exploring gut
pathophysiology for novel therapeutic targets. Transl Res.
176:38–68. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
45
|
Geremia A, Biancheri P, Allan P, Corazza
GR and Di Sabatino A: Innate and adaptive immunity in inflammatory
bowel disease. Autoimmun Rev. 13:3–10. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
46
|
Speca S, Rousseaux C, Dubuquoy C, Rieder
F, Vetuschi A, Sferra R, Giusti I, Bertin B, Dubuquoy L, Gaudio E,
et al: Novel PPARγ modulator GED-0507-34 levo ameliorates
inflammation-driven intestinal fibrosis. Inflamm Bowel Dis.
22:279–292. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
47
|
Rieder F and Fiocchi C: Intestinal
fibrosis in IBD - a dynamic, multifactorial process. Nat Rev
Gastroenterol Hepatol. 6:228–235. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
48
|
Andersen V, Nimmo E, Krarup HB, Drummond
H, Christensen J, Ho GT, Ostergaard M, Ernst A, Lees C, Jacobsen
BA, et al: Cyclooxygenase-2 (COX-2) polymorphisms and risk of
inflammatory bowel disease in a Scottish and Danish case-control
study. Inflamm Bowel Dis. 17:937–946. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
49
|
Østergaard M, Ernst A, Labouriau R,
Dagiliené E, Krarup HB, Christensen M, Thorsgaard N, Jacobsen BA,
Tage-Jensen U, Overvad K, et al: Cyclooxygenase-2, multidrug
resistance 1, and breast cancer resistance protein gene
polymorphisms and inflammatory bowel disease in the Danish
population. Scand J Gastroenterol. 44:65–73. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
50
|
Cox DG, Crusius JB, Peeters PH,
Bueno-de-Mesquita HB, Pena AS and Canzian F: Haplotype of
prostaglandin synthase 2/cyclooxygenase 2 is involved in the
susceptibility to inflammatory bowel disease. World J
Gastroenterol. 11:6003–6008. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
51
|
Garrity-Park MM, Loftus EV Jr, Bryant SC
and Smyrk TC: A biomarker panel to detect synchronous neoplasm in
non-neoplastic surveillance biopsies from patients with ulcerative
colitis. Inflamm Bowel Dis. 22:1568–1574. 2016. View Article : Google Scholar : PubMed/NCBI
|
