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Diet-induced hypoxia responsive element demethylation increases CEACAM6 expression, favouring Crohn's disease-associated Escherichia coli colonisation
  1. Jérémy Denizot1,2,
  2. Alexis Desrichard3,
  3. Allison Agus1,2,
  4. Nancy Uhrhammer3,
  5. Nicolas Dreux1,2,
  6. Valérie Vouret-Craviari4,5,
  7. Paul Hofman4,5,6,
  8. Arlette Darfeuille-Michaud1,2,7,8,
  9. Nicolas Barnich1,2,7
  1. 1Clermont Université, M2iSH, UMR 1071 INSERM/Université d'Auvergne, Clermont-Ferrand, France
  2. 2Unité Sous Contrat 2018 Institut National de la Recherche Agronomique, Clermont-Ferrand, France
  3. 3Departments of Oncogenetics and Breast Oncology, Centre Jean Perrin, Clermont-Ferrand, France
  4. 4Institute for Research on Cancer and aging (IRCAN), Nice, France
  5. 5University of Nice-Sophia Antipolis, Nice, France
  6. 6Laboratory of Clinical and Experimental Pathology and Human Biobank, Pasteur Hospital, Nice, France
  7. 7Institut Universitaire de Technologie, Génie Biologique, Aubière, France
  8. 8Centre Hospitalier Universitaire Clermont-Ferrand, France
  1. Correspondence to Dr Nicolas Barnich, M2iSH, UMR 1071 Inserm/Université d'Auvergne, CBRV, 28 place Henri Dunant, Clermont-Ferrand 63001, France; nicolas.barnich{at}


Objective Adherent-invasive Escherichia coli (AIEC) are abnormally predominant on Crohn's disease (CD) ileal mucosa. AIEC strains adhere to enterocytes via interaction between type 1 pili and CEACAM6 receptors abnormally expressed on CD ileal mucosa, leading to gut inflammation. We analysed whether epigenetic mechanisms are involved in the upregulation of CEACAM6 expression in intestinal epithelial cells (IECs).

Design Methylation of CEACAM6 promoter was analysed using bisulfite sequencing and site-specific methylation by SnapShot. pCpGfree reporter system was used to analyse CEACAM6 promoter activity. Transgenic mice expressing human CEACAM6 fed either standard food or a low-methyl diet (LMD) were orally challenged with 109 AIEC LF82. After 3 days, gut-associated AIEC and proinflammatory cytokines were quantified.

Results Analysis of CEACAM6 gene promoter revealed potentially methylated dinucleotide CpGs within HIF-1-responsive elements (HREs). Methylation levels of CpG within CEACAM6 promoter were inversely correlated with CEACAM6 expression in IEC expressing various levels of CEACAM6. We show the critical role of HRE methylation and transcription factor HIF-1 in the regulation of CEACAM6 gene in IEC. This was confirmed in transgenic mice expressing human CEACAM6 fed a LMD. LMD-dependent HRE demethylation led to abnormal gut expression of CEACAM6, favouring AIEC colonisation and subsequent inflammation.

Conclusions HRE hypomethylation in CEACAM6 promoter correlates with high expression in IEC. Our findings suggest that abnormal DNA methylation leading to CEACAM6 increased expression and AIEC-mediated gut inflammation can be related to changes in nutritional habits, such as low intake in methyl donor molecules, leading to abnormal epigenetic marks in mouse model mimicking CD susceptibility.


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