Epigenetic master regulators HDAC1 and HDAC5 control pathobiont Enterobacteria colonization in ileal mucosa of Crohn's disease patients
Mélissa Chervy, Adeline Sivignon, Flavie Dambrine, Anthony Buisson, Pierre Sauvanet, Catherine Godfraind, Matthieu Allez, Lionel Le Bourhis, The Remind Group, Nicolas Barnich, Jérémy Denizot, Mélissa Chervy, Adeline Sivignon, Flavie Dambrine, Anthony Buisson, Pierre Sauvanet, Catherine Godfraind, Matthieu Allez, Lionel Le Bourhis, The Remind Group, Nicolas Barnich, Jérémy Denizot
Abstract
AIEC Adherent-Invasive Escherichia coli; BSA Bovine serum albumin; CD Crohn's disease; CEABAC10 Carcinoembryonic antigen bacterial artificial chromosome 10; CEACAM Carcinoembryonic antigen-related cell adhesion molecule; FBS Fetal bovine serum; IBD Inflammatory Bowel Disease; HAT Histone acetyltransferase; HDAC Histone deacetylase; kDa KiloDalton; SAHA Suberoylanilide Hydroxamic Acid; Scr Scramble.
Keywords: Adherent-InvasiveE. coli; Crohn’s disease; High-fat diet; Histone deacetylases; histone acetylation.
Conflict of interest statement
The authors report there are no conflict of interest to declare.
Figures
References
- Torres J, Mehandru S, Colombel J-F P-BL.. Crohn’s disease. The Lancet. 2017;389:1741–20. doi:10.1016/S0140-6736(16)31711-1.
- Ng SC, Shi HY, Hamidi N, Underwood FE, Tang W, Benchimol EI, Panaccione R, Ghosh S, Wu JCY, Chan FKL, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. The Lancet. 2017;390(10114):2769–2778. doi:10.1016/S0140-6736(17)32448-0.
- DʼSouza S, Levy E, Mack D, Israel D, Lambrette P, Ghadirian P, Deslandres C, Morgan K, Seidman EG, Amre DK. Dietary patterns and risk for Crohnʼs disease in children. Inflamm Bowel Dis. 2008;14(3):367–373. doi:10.1002/ibd.20333.
- Chiba M, Nakane K, Komatsu M. Westernized diet is the most ubiquitous environmental factor in inflammatory bowel disease. Perm J. 2019;23(1):18–107. doi:10.7812/TPP/18-107.
- Lo C-H, Lochhead P, Khalili H, Song M, Tabung FK, Burke KE, Richter JM, Giovannucci EL, Chan AT, Ananthakrishnan AN. Dietary inflammatory potential and risk of Crohn’s disease and ulcerative colitis. Gastroenterology. 2020;159(3):873–883.e1. doi:10.1053/j.gastro.2020.05.011.
- Narula N, Wong ECL, Dehghan M, Mente A, Rangarajan S, Lanas F, Lopez-Jaramillo P, Rohatgi P, Lakshmi PVM, Varma RP, et al. Association of ultra-processed food intake with risk of inflammatory bowel disease: prospective cohort study. BMJ. 2021;374:n1554. doi:10.1136/bmj.n1554.
- Gill PA, Inniss S, Kumagai T, Rahman FZ, Smith AM. The role of diet and gut microbiota in regulating gastrointestinal and inflammatory disease. Front Immunol. 2022;13:866059. doi:10.3389/fimmu.2022.866059.
- Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, Yantiss R, Orsi RH, Wiedmann M, McDonough P, Kim SG, et al. Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn’s disease involving the ileum. ISME J. 2007;1(5):403–418. doi:10.1038/ismej.2007.52.
- Khanna S, Raffals LE. The Microbiome in Crohn’s Disease. Gastroenterol Clin North Am. 2017;46(3):481–492. doi:10.1016/j.gtc.2017.05.004.
- Sokol H, Brot L, Stefanescu C, Auzolle C, Barnich N, Buisson A, Fumery M, Pariente B, Le Bourhis L, Treton X, et al. Prominence of ileal mucosa-associated microbiota to predict postoperative endoscopic recurrence in Crohn’s disease. Gut. 2020;69:462–472. doi:10.1136/gutjnl-2019-318719.
- Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser A-L, Barnich N, Bringer M-A, Swidsinski A, Beaugerie L, Colombel J-F. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterology. 2004;127:412–421. doi:10.1053/j.gastro.2004.04.061.
- Martinez-Medina M, Aldeguer X, Lopez-Siles M, González-Huix F, López-Oliu C, Dahbi G, Blanco JE, Blanco J, Garcia-Gil LJ, Darfeuille-Michaud A. Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. Coli (AIEC) in Crohn’s Disease Inflamm Bowel Dis. 2009;15:872–882. doi:10.1002/ibd.20860.
- Palmela C, Chevarin C, Xu Z, Torres J, Sevrin G, Hirten R, Barnich N, Ng SC, Colombel J-F. Adherent-invasive Escherichia coli in inflammatory bowel disease. Gut. 2018;67:574–587. doi:10.1136/gutjnl-2017-314903.
- Denizot J, Sivignon A, Barreau F, Darcha C, Chan HFC, Stanners CP, Hofman P, Darfeuille-Michaud A, Adherent-invasive BN. Escherichia coli induce claudin-2 expression and barrier defect in CEABAC10 mice and Crohn’s disease patients. Inflamm Bowel Dis. 2012;18:294–304. doi:10.1002/ibd.21787.
- Chervy M, Barnich N, Denizot J. Adherent-Invasive E. Coli: Update on the Lifestyle of a Troublemaker in Crohn’s Disease. Int J Mol Sci. 2020;21:3734.
- Martinez-Medina M, Denizot J, Dreux N, Robin F, Billard E, Bonnet R, Darfeuille-Michaud A, Barnich N. Western diet induces dysbiosis with increased E coli in CEABAC10 mice, alters host barrier function favouring AIEC colonisation. Gut. 2014;63:116–124. doi:10.1136/gutjnl-2012-304119.
- Agus A, Denizot J, Thévenot J, Martinez-Medina M, Massier S, Sauvanet P, Bernalier-Donadille A, Denis S, Hofman P, Bonnet R, et al. Western diet induces a shift in microbiota composition enhancing susceptibility to Adherent-Invasive E. Coli Infection and Intestinal Inflammation. Sci Rep. 2016;6:19032.
- Wehkamp J, Salzman NH, Porter E, Nuding S, Weichenthal M, Petras RE, Shen B, Schaeffeler E, Schwab M, Linzmeier R, et al. Reduced Paneth cell α-defensins in ileal Crohn’s disease. Proc Natl Acad Sci U S A. 2005;102:18129–18134. doi:10.1073/pnas.0505256102.
- Wehkamp J, Stange EF. Paneth’s disease. J Crohns Colitis. 2010;4:523–531. doi:10.1016/j.crohns.2010.05.010.
- Stappenbeck TS, McGovern DPB. Paneth cell alterations in the development and phenotype of Crohn’s disease. Gastroenterology. 2017;152(2):322–326. doi:10.1053/j.gastro.2016.10.003.
- Alkaissi LY, Winberg ME, Heil SDS, Haapaniemi S, Myrelid P, Stange EF, Söderholm JD, Keita ÅV. Antagonism of Adherent Invasive E. Coli LF82 with Human a-defensin 5 in the Follicle-associated Epithelium of Patients with Ileal Crohn’s Disease. Inflamm Bowel Dis. 2020;27:1116–1127.
- McPhee JB, Small CL, Reid-Yu SA, Brannon JR, Le Moual H, Coombes BK. Host defense peptide resistance contributes to colonization and maximal intestinal pathology by Crohn’s disease-associated adherent-Invasive Escherichia coli. Infect Immun. 2014;82(8):3383–3393. doi:10.1128/IAI.01888-14.
- Lin Z, Hegarty JP, Cappel JA, Yu W, Chen X, Faber P, Wang Y, Kelly AA, Poritz LS, Peterson BZ, et al. Identification of disease-associated DNA methylation in intestinal tissues from patients with inflammatory bowel disease. Clin Genet. 2011;80(1):59–67. doi:10.1111/j.1399-0004.2010.01546.x.
- Ventham NT, Kennedy NA, Adams AT, Kalla R, Heath S, O’Leary KR, Drummond H, Wilson DC, Gut IG, Nimmo ER, et al. Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease. Nat Commun. 2016;7(1):13507. doi:10.1038/ncomms13507.
- Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo B-K, Kumar N, Lawley T, et al. DNA methylation and transcription patterns in intestinal epithelial cells from pediatric patients with inflammatory bowel diseases differentiate disease subtypes and associate with outcome. Gastroenterology. 2018;154(3):585–598. doi:10.1053/j.gastro.2017.10.007.
- Somineni HK, Venkateswaran S, Kilaru V, Marigorta UM, Mo A, Okou DT, Kellermayer R, Mondal K, Cobb D, Walters TD, et al. Blood-Derived DNA methylation signatures of Crohn’s disease and severity of intestinal inflammation. Gastroenterology. 2019;156(8):2254–2265.e3. doi:10.1053/j.gastro.2019.01.270.
- Moret-Tatay I, Cerrillo E, Sáez-González E, Hervás D, Iborra M, Sandoval J, Busó E, Tortosa L, Nos P, Beltrán B. Identification of epigenetic methylation signatures with clinical value in Crohnʼs disease. Clin Transl Gastroenterol. 2019;10(10):e00083. doi:10.14309/ctg.0000000000000083.
- Serena C, Millan M, Ejarque M, Saera-Vila A, Maymó-Masip E, Núñez-Roa C, Monfort-Ferré D, Terrón-Puig M, Bautista M, Menacho M, et al. Adipose stem cells from patients with Crohn’s disease show a distinctive DNA methylation pattern. Clin Epigenetics. 2020;12(1):53. doi:10.1186/s13148-020-00843-3.
- Hornschuh M, Wirthgen E, Wolfien M, Singh KP, Wolkenhauer O, Däbritz J. The role of epigenetic modifications for the pathogenesis of Crohn’s disease. Clin Epigenetics. 2021;13(1):108. doi:10.1186/s13148-021-01089-3.
- Seto E, Yoshida M. Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harb Perspect Biol. 2014;6(4):a018713. doi:10.1101/cshperspect.a018713.
- Park S-Y, Kim J-S. A short guide to histone deacetylases including recent progress on class II enzymes. Exp Mol Med. 2020;52(2):204–212. doi:10.1038/s12276-020-0382-4.
- Turgeon N, Blais M, Gagné J-M, Tardif V, Boudreau F, Perreault N, Asselin C . HDAC1 and HDAC2 restrain the intestinal inflammatory response by regulating intestinal epithelial cell differentiation. PLoS ONE. 2013;8(9):e73785. doi:10.1371/journal.pone.0073785.
- Turgeon N, Gagné JM, Blais M, Gendron F-P, Boudreau F, Asselin C. The acetylome regulators Hdac1 and Hdac2 differently modulate intestinal epithelial cell dependent homeostatic responses in experimental colitis. Am J Physiol-Gastrointest Liver Physiol. 2014;306(7):G594–605. doi:10.1152/ajpgi.00393.2013.
- Gonneaud A, Turgeon N, Jones C, Couture C, Lévesque D, Boisvert F-M, Boudreau F, Asselin C. HDAC1 and HDAC2 independently regulate common and specific intrinsic responses in murine enteroids. Sci Rep. 2019;9(1):5363. doi:10.1038/s41598-019-41842-6.
- Gonneaud A, Turgeon N, Boisvert F-M, Boudreau F, Asselin C. JAK-STAT pathway inhibition partially restores intestinal homeostasis in Hdac1- and Hdac2-intestinal epithelial cell-deficient mice. Cells. 2021;10(2):224. doi:10.3390/cells10020224.
- Alenghat T, Osborne LC, Saenz SA, Kobuley D, Ziegler CGK, Mullican SE, Choi I, Grunberg S, Sinha R, Wynosky-Dolfi M, et al. Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis. Nature. 2013;504(7478):153–157. doi:10.1038/nature12687.
- Tsaprouni LG, Ito K, Powell JJ, Adcock IM, Punchard N. Differential patterns of histone acetylation in inflammatory bowel diseases. Journal of Inflammation. 2011;8(1):1. doi:10.1186/1476-9255-8-1.
- Friedrich M, Gerbeth L, Gerling M, Rosenthal R, Steiger K, Weidinger C, Keye J, Wu H, Schmidt F, Weichert W, et al. HDAC inhibitors promote intestinal epithelial regeneration via autocrine TGFβ1 signalling in inflammation. Mucosal Immunol. 2019;12(3):656–667. doi:10.1038/s41385-019-0135-7.
- Buisson A, Sokol H, Hammoudi N, Nancey S, Treton X, Nachury M, Fumery M, Hébuterne X, Rodrigues M, Hugot J-P, et al. Role of adherent and invasive Escherichia coli in Crohn’s disease: lessons from the postoperative recurrence model. Gut. pp.gutjnl-2021–325971. 2022. doi:10.1136/gutjnl-2021-325971
- Chan CHF, Stanners CP. Novel mouse model for carcinoembryonic antigen-based therapy. Mol Ther J Am Soc Gene Ther. 2004;9(6):775–785. doi:10.1016/j.ymthe.2004.03.009.
- Carvalho FA, Barnich N, Sivignon A, Darcha C, Chan CHF, Stanners CP, Darfeuille-Michaud A. Crohn’s disease adherent-invasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM. J Exp Med. 2009;206(10):2179–2189. doi:10.1084/jem.20090741.
- Ngollo M, Perez K, Hammoudi N, Gorelik Y, Delord M, Auzolle C, Bottois H, Cazals-Hatem D, Bezault M, Nancey S, et al. Identification of gene expression profiles associated with an increased risk of post-operative recurrence in Crohn’s disease. J Crohns Colitis. 2022;16(8):1269–80. doi:10.1093/ecco-jcc/jjac021.
- Eskandarian HA, Impens F, Nahori M-A, Soubigou G, Coppée J-Y, Cossart P, Hamon MA. A role for SIRT2-dependent histone H3K18 deacetylation in bacterial infection. Science. 2013;341(6145):1238858. doi:10.1126/science.1238858.
- Mombelli M, Lugrin J, Rubino I, Chanson A-L, Giddey M, Calandra T, Roger T. Histone deacetylase inhibitors impair antibacterial defenses of macrophages. J Infect Dis. 2011;204(9):1367–1374. doi:10.1093/infdis/jir553.
- Corrêa RO, Vieira A, Sernaglia EM, Lancellotti M, Vieira AT, Avila-Campos MJ, Rodrigues HG, Vinolo MAR. Bacterial short-chain fatty acid metabolites modulate the inflammatory response against infectious bacteria. Cell Microbiol. 2017;19(7):e12720. doi:10.1111/cmi.12720.
- Ormsby MJ, Logan M, Johnson SA, McIntosh A, Fallata G, Papadopoulou R, Papachristou E, Hold GL, Hansen R, Ijaz UZ, et al. Inflammation associated ethanolamine facilitates infection by Crohn’s disease-linked adherent-invasive Escherichia coli. EBioMedicine. 2019;43:325–332. doi:10.1016/j.ebiom.2019.03.071.
- Baldelli V, Scaldaferri F, Putignani L, Del Chierico F. The role of enterobacteriaceae in gut microbiota dysbiosis in inflammatory bowel diseases. Microorganisms. 2021;9(4):697. doi:10.3390/microorganisms9040697.
- Li B, Zhang L, Zhu L, Cao Y, Dou Z, Yu Q. HDAC5 promotes intestinal sepsis via the Ghrelin/E2F1/NF-κB axis. FASEB J Off Publ Fed Am Soc Exp Biol. 2021;35:e21368.
- Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJM, Faber KN, Hermoso MA. Short Chain Fatty Acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol. 2019;10:277. doi:10.3389/fimmu.2019.00277.
- Downes M, Ordentlich P, Kao H-Y, Alvarez JGA, Evans RM. Identification of a nuclear domain with deacetylase activity. Proc Natl Acad Sci U S A. 2000;97(19):10330–10335. doi:10.1073/pnas.97.19.10330.
- Zhang L, Deng M, Lu A, Chen Y, Chen Y, Wu C, Tan Z, Boini KM, Yang T, Zhu Q, et al. Sodium butyrate attenuates angiotensin II-induced cardiac hypertrophy by inhibiting COX2/PGE2 pathway via a HDAC5/HDAC6-dependent mechanism. J Cell Mol Med. 2019;23(12):8139–8150. doi:10.1111/jcmm.14684.
- Buisson A, Vazeille E, Fumery M, Pariente B, Nancey S, Seksik P, Peyrin‐Biroulet L, Allez M, Ballet N, Filippi J, et al. Faster and less invasive tools to identify patients with ileal colonization by adherent-invasive E. coli in Crohn’s disease. United European Gastroenterology Journal. 2021;9(9):1007–1018. doi:10.1002/ueg2.12161.
- Auzolle C, Nancey S, Tran-Minh M-L, Buisson A, Pariente B, Stefanescu C, Fumery M, Marteau P, Treton X, Hammoudi N, et al. Male gender, active smoking and previous intestinal resection are risk factors for post-operative endoscopic recurrence in Crohn’s disease: results from a prospective cohort study. Aliment Pharmacol Ther. 2018;48:924–932. doi:10.1111/apt.14944.
Source: PubMed