J. Carrière, A. Darfeuille-michaud, and H. T. Nguyen, Infectious etiopathogenesis of Crohn's disease, World J. Gastroenterol, vol.20, pp.12102-12117, 2014.

S. F. Øyri, G. M?zes, and F. Sipos, Dysbiotic gut microbiome: A key element of Crohn's disease, Comp. Immunol. Microbiol. Infect. Dis, vol.43, pp.36-49, 2015.

C. L. O'brien, M. Bringer, K. E. Holt, D. M. Gordon, A. L. Dubois et al., Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli, vol.66, pp.1382-1389, 2017.

A. Darfeuille-michaud, J. Boudeau, P. Bulois, C. Neut, A. Glasser et al., High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease, Gastroenterology, vol.127, pp.412-421, 2004.

B. Chassaing, N. Rolhion, A. De-vallée, S. Y. Salim, M. Prorok-hamon et al., Crohn disease-associated adherent-invasive E. coli bacteria target mouse and human Peyer's patches via long polar fimbriae, J. Clin. Investig, vol.121, pp.966-975, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02650093

A. L. Glasser, J. Boudeau, N. Barnich, M. H. Perruchot, J. F. Colombel et al., Adherent invasive Escherichia coli strains from patients with Crohn's disease survive and replicate within macrophages without inducing host cell death, Infect. Immun, vol.69, pp.5529-5537, 2001.

E. Vazeille, A. Buisson, M. A. Bringer, M. Goutte, L. Ouchchane et al., Monocyte-derived macrophages from Crohn's disease patients are impaired in the ability to control intracellular adherent-invasive Escherichia coli and exhibit disordered cytokine secretion profile, J. Crohn Colitis, vol.9, pp.410-420, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01594239

H. T. Nguyen, G. Dalmasso, S. Müller, J. Carrière, F. Seibold et al., Crohn's disease-associated adherent invasive escherichia coli modulate levels of microRNAs in intestinal epithelial cells to reduce autophagy, Gastroenterology, vol.146, pp.508-519, 2014.

P. Lapaquette, A. Glasser, A. Huett, R. J. Xavier, and A. Darfeuille-michaud, Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly, Cell. Microbiol, vol.12, pp.99-113, 2010.

P. Lapaquette, M. Bringer, and A. Darfeuille-michaud, Defects in autophagy favour adherent-invasive Escherichia coli persistence within macrophages leading to increased pro-inflammatory response, Cell. Microbiol, vol.14, pp.791-807, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01227409

F. A. Carvalho, N. Barnich, A. Sivignon, C. Darcha, C. H. Chan et al., Crohn's disease adherent-invasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM, J. Exp. Med, vol.206, pp.2179-2189, 2009.

M. Martinez-medina, J. Denizot, N. Dreux, F. Robin, E. Billard et al., Western diet induces dysbiosis with increased e coli in CEABAC10 mice, alters host barrier function favouring AIEC colonisation, Gut, vol.63, pp.116-124, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01928324

A. Bretin, C. Lucas, A. Larabi, G. Dalmasso, E. Billard et al., AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation, Sci. Rep, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01897658

A. Bretin, J. Carrière, G. Dalmasso, A. Bergougnoux, W. B'chir et al., Activation of the EIF2AK4-EIF2A/eIF2?-ATF4 pathway triggers autophagy response to Crohn disease-associated adherent-invasive Escherichia coli infection, Autophagy, vol.12, pp.770-783, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02640052

G. Dalmasso, H. T. Nguyen, T. Faïs, S. Massier, N. Barnich et al., Crohn's Disease-Associated Adherent-Invasive Escherichia coli Manipulate Host Autophagy by Impairing SUMOylation, vol.8, p.35, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02060087

, Microorganisms 2020, vol.8, p.1205

A. Larabi, N. Barnich, and H. T. Nguyen, New insights into the interplay between autophagy, gut microbiota and inflammatory responses in IBD, Autophagy, vol.16, pp.38-51, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02193636

J. Carrière, A. Bretin, A. Darfeuille-michaud, N. Barnich, and H. T. Nguyen, Exosomes Released from Cells Infected with Crohn's Disease-associated Adherent-Invasive Escherichia coli Activate Host Innate Immune Responses and Enhance Bacterial Intracellular Replication, Inflamm. Bowel Dis, vol.22, pp.516-528, 2016.

A. Larabi, G. Dalmasso, J. Delmas, N. Barnich, and H. T. Nguyen, Exosomes transfer miRNAs from cell-to-cell to inhibit autophagy during infection with Crohn's disease-associated adherent-invasive E. coli, Gut Microbes, vol.11, pp.1677-1694, 2020.

S. Moein, M. Vaghari-tabari, D. Qujeq, M. Majidinia, S. M. Nabavi et al., MiRNAs and inflammatory bowel disease: An interesting new story, J. Cell. Physiol, vol.234, pp.3277-3293, 2019.

P. Brest, P. Lapaquette, M. Souidi, K. Lebrigand, A. Cesaro et al., A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease, Nat. Genet, vol.43, pp.242-245, 2011.

B. C. Morson, The early histological lesion of Crohn's disease, Proc. R. Soc. Med, vol.65, pp.71-72, 1972.

E. Gullberg and J. D. Söderholm, Peyer's patches and M cells as potential sites of the inflammatory onset in Crohn's disease, Ann. N. Y. Acad. Sci, vol.1072, pp.218-232, 2006.

Y. Nakamura, S. Kimura, and K. Hase, M cell-dependent antigen uptake on follicle-associated epithelium for mucosal immune surveillance, Inflamm. Regen, vol.38, pp.1-9, 2018.

Å. Keita, S. Salim, T. Jiang, P. Yang, L. Franzén et al., Increased uptake of non-pathogenic E. coli via the follicle-associated epithelium in longstanding ileal Crohn's disease, J. Pathol, vol.215, pp.135-144, 2008.

S. Y. Salim, M. A. Silva, Å. V. Keita, M. Larsson, P. Andersson et al., CD83+CCR7? Dendritic Cells Accumulate in the Subepithelial Dome and Internalize Translocated Escherichia coli HB101 in the Peyer's Patches of Ileal Crohn's Disease, Am. J. Pathol, vol.174, pp.82-90, 2009.

E. Vazeille, B. Chassaing, A. Buisson, A. Dubois, A. De-vallée et al., GipA Factor Supports Colonization of Peyer's Patches by Crohn's Disease-associated Escherichia coli, Inflamm. Bowel Dis, vol.22, pp.68-81, 2016.

C. L. Roberts, A. V. Keita, S. H. Duncan, N. Kennedy, J. D. Soderholm et al., Translocation of Crohn's disease Escherichia coli across M-cells: Contrasting effects of soluble plant fibres and emulsifiers, Gut, vol.59, pp.1331-1339, 2010.

L. Etienne-mesmin, B. Chassaing, P. Sauvanet, J. Denizot, S. Blanquet-diot et al., Interactions with M cells and macrophages as key steps in the pathogenesis of enterohemorragic Escherichia coli infections, PLoS ONE, vol.6, 2011.

B. Dogan, H. Suzuki, D. Herlekar, B. R. Sartor, B. J. Campbell et al., Inflammation-associated adherent-invasive escherichia coli are enriched in pathways for use of propanediol and iron and M-cell translocation, Inflamm. Bowel Dis, vol.20, pp.1919-1932, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01332099

A. Darfeuille-michaud, C. Neut, N. Barnich, E. Lederman, P. Di-martino et al., Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease, Gastroenterology, vol.115, pp.1405-1413, 1998.

H. Dweep, C. Sticht, P. Pandey, and N. Gretz, miRWalk-Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes, J. Biomed. Inform, vol.44, pp.839-847, 2011.

Y. Fujimura, R. Kamoi, and M. Iida, Pathogenesis of aphthoid ulcers in Crohn's disease: Correlative findings by magnifying colonoscopy, electron microscopy, and immunohistochemistry, Gut, vol.38, pp.724-732, 1996.

D. Silva, C. Wagner, C. Bonnardel, J. Gorvel, J. P. Lelouard et al., The Peyer's patch mononuclear phagocyte system at steady state and during infection, Front. Immunol, 1254.

M. Viladomiu, R. Hontecillas, M. Pedragosa, A. Carbo, S. Hoops et al., Modeling the Role of Peroxisome Proliferator-Activated Receptor ? and MicroRNA-146 in Mucosal Immune Responses to Clostridium difficile, PLoS ONE, vol.7, 2012.

S. F. Cheng, L. Li, and L. M. Wang, miR-155 and miR-146b negatively regulates IL6 in Helicobacter pylori (cagA+) infected gastroduodenal ulcer, Eur. Rev. Med. Pharmacol. Sci, vol.19, pp.607-613, 2015.

J. Hanwei, X. Nie, H. Zhu, B. Li, F. Pang et al., miR-146b-5p Plays a Critical Role in the Regulation of Autophagy in ?per Brucella melitensis -Infected RAW264.7 Cells, Biomed Res. Int, pp.1-16, 2020.

L. Y. Wu, X. P. Ma, Y. Shi, C. H. Bao, X. M. Jin et al., Alterations in microRNA expression profiles in inflamed and noninflamed ascending colon mucosae of patients with active Crohn's disease, J. Gastroenterol. Hepatol, vol.32, pp.1706-1715, 2017.

P. Chen, Y. Li, L. Li, Q. Yu, K. Chao et al., Circulating microRNA146b-5p is superior to C-reactive protein as a novel biomarker for monitoring inflammatory bowel disease, Aliment. Pharmacol. Ther, vol.49, pp.733-743, 2019.

S. Lapthorne, J. Macsharry, P. Scully, K. Nally, and F. Shanahan, Differential intestinal M-cell gene expression response to gut commensals, Immunology, vol.136, pp.312-324, 2012.

K. Wang, C. Huang, C. Huang, and S. Fang, Impacts of Salmonella enterica Serovar Typhimurium and Its speG Gene on the Transcriptomes of In Vitro M Cells and Caco-2 Cells, PLoS ONE, vol.11, 2016.

O. Hitotsumatsu, R. Ahmad, R. Tavares, M. Wang, D. Philpott et al., The Ubiquitin-Editing Enzyme A20 Restricts Nucleotide-Binding Oligomerization Domain Containing 2-Triggered Signals, Immunity, vol.28, pp.381-390, 2008.

N. Oshima, S. Ishihara, M. A. Rumi, M. M. Aziz, Y. Mishima et al., A20 is an early responding negative regulator of Toll-like receptor 5 signalling in intestinal epithelial cells during inflammation, Clin. Exp. Immunol, vol.159, pp.185-198, 2010.

L. E. Kolodziej, J. P. Lodolce, J. E. Chang, J. R. Schneider, W. A. Grimm et al., TNFAIP3 Maintains Intestinal Barrier Function and Supports Epithelial Cell Tight Junctions, PLoS ONE, vol.6, 2011.

Y. Shi, Y. Guo, J. Zhou, L. Wu, L. Chen et al., Herbs-partitioned moxibustion improves intestinal epithelial tight junctions by upregulating A20 expression in a mouse model of Crohn's disease, Biomed. Pharmacother, vol.118, 2019.

L. Vereecke, S. Vieira-silva, T. Billiet, J. H. Van-es, C. Mc-guire et al., A20 controls intestinal homeostasis through cell-specific activities, Nat. Commun, vol.5, p.5103, 2014.

S. Bartfeld, T. Bayram, M. Van-de-wetering, M. Huch, H. Begthel et al., In Vitro Expansion of Human Gastric Epithelial Stem Cells and Their Responses to Bacterial Infection, Gastroenterology, vol.148, pp.126-136, 2015.

S. M. Camp, E. Ceco, C. L. Evenoski, S. M. Danilov, T. Zhou et al., Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NF? B Signaling and Inflammatory Lung Injury, Sci. Rep, vol.5, pp.1-14, 2015.

K. Neubauer, I. Bednarz-misa, E. Walecka-zacharska, J. Wierzbicki, A. Agrawal et al., Oversecretion and Overexpression of Nicotinamide Phosphoribosyltransferase/Pre-B Colony-Enhancing Factor/Visfatin in Inflammatory Bowel Disease Reflects the Disease Activity, Severity of Inflammatory Response and Hypoxia, Int. J. Mol. Sci, vol.20, 2019.

K. Terahara, M. Yoshida, O. Igarashi, T. Nochi, G. S. Pontes et al., Comprehensive gene expression profiling of Peyer's patch M cells, villous M-like cells, and intestinal epithelial cells, J. Immunol, vol.180, pp.7840-7846, 2008.

G. Nakato, S. Fukuda, K. Hase, R. Goitsuka, M. D. Cooper et al., New Approach for M-Cell-Specific Molecules Screening by Comprehensive Transcriptome Analysis, DNA Res, vol.16, pp.227-235, 2009.

S. Pesce, M. Squillario, M. Greppi, F. Loiacono, L. Moretta et al., New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression, Front. Immunol, vol.9, pp.1-18, 2018.

N. Saki, S. Abroun, M. Soleimani, Y. Mortazavi, S. Kaviani et al., The roles of miR-146a in the differentiation of Jurkat T-lymphoblasts, Hematology, vol.19, pp.141-147, 2014.

J. C. Hardwick, . Van-den, G. R. Brink, S. A. Bleuming, I. Ballester et al., Bone morphogenetic protein 2 is expressed by, and acts upon, mature epithelial cells in the colon, Gastroenterology, vol.126, pp.111-121, 2004.

Y. Ben-shahar, Z. Abassi, H. Kreizman-shefer, Y. Pollak, U. Bhattacharya et al., Accelerated Intestinal Epithelial Cell Turnover Correlates with Stimulated BMP Signaling Cascade following Intestinal Ischemia-Reperfusion in a Rat, Eur. J. Pediatr. Surg, vol.30, pp.64-070, 2020.

S. Oguchi, W. A. Walker, and I. R. Sanderson, Differentiation and Polarity Alter the Binding of IGF-I to Human Intestinal Epithelial (Caco-2) Cells, J. Pediatr. Gastroenterol. Nutr, vol.20, pp.148-155, 1995.

A. E. Kartikasari, J. X. Zhou, M. S. Kanji, D. N. Chan, A. Sinha et al., The histone demethylase Jmjd3 sequentially associates with the transcription factors Tbx3 and Eomes to drive endoderm differentiation, EMBO J, vol.32, pp.1393-1408, 2013.

B. Y. Lam and S. Chawla, MEF2D expression increases during neuronal differentiation of neural progenitor cells and correlates with neurite length, Neurosci. Lett, vol.427, pp.153-158, 2007.

V. Runfola, S. Sebastian, F. J. Dilworth, and D. Gabellini, Rbfox proteins regulate tissue-specific alternative splicing of Mef2D required for muscle differentiation, © 2020 by the authors. Licensee MDPI, vol.128, pp.631-637, 2015.