Medico - Scientific Background
The gut microbiota is composed of a huge number of diverse bacterial communities (Bacteroidetes and Firmicutes are the dominant phyla) and of abundant fungi. In humans, the coexistence of resident commensals and host cells play a beneficial role in regulating both energy harvesting from nutrients and host defense. Notably, the intestinal microbiota is able to regulate virulence of enteric bacterial pathogens, including Citrobacter rodentium. However, not all commensals are able to maintain quiescent and protective immunity, arguing for the need to decipher the nature and mechanisms of these processes.
The nucleotide-binding oligomerization domain containing protein 2 (Nod2) is thought to play a decisive role in maintaining microbial tolerance and host defense at the intestinal barrier through two adaptor proteins, namely Ripk2 and Card9, but its role in inciting innate and adaptive immunity is complex. Noteworthy, Nod2 and Card9 variants have been associated with Crohn’s disease (CD). More recently, we unveiled a key role of Nod2-driven dysbiosis in predisposing to intestinal inflammation (Couturier-Maillard, et al JCI 2013). More importantly, genetic ablation of either Nod2 (preliminary data) or Card9 (Sokol et al. Gastroenterology 2013) results in abnormal host defense against C. rodentium.
Based on such current state of the art, the C. rodentium-driven colitis model is of high interest as appropriate response to such enteric bacterial pathogen requires many major biological processes involved in the maintenance of intestinal homeostasis and that are altered in CD.
However, the cellular and molecular mechanism whereby Nod2 and/or Card9 may control pathogen virulence by shaping a non-permissive microbiota has not been investigated yet.
Through a multidisciplinary approach, the main objective of the current proposal is therefore to decipher the microbiota-dependent and -independent mechanisms by which the pathogenesis of enteric pathogen bacteria is regulated.
To achieve our objective, we envisage an integrated “microbiome/immunology” approach by taking advantage of gnotobiotic animals and by using cre-lox and high-throughput sequencing technologies, as well as developing multidimensional statistical models to decipher the dynamic balance established between the commensal microbiota and the host immune system. Notably, we will use transgenic models of dysbiotic microbiota (ie. Nod2 and Card9 deficient mice) and C. rodentium, as an experimental model microorganism. Whereas most of the studies on this topic so far analyzed either the bacterial gut microbiota or the host response, our ambitious strategy is mainly based on the concomitant analysis of gut microbiota (bacterial but also fungal part) and host compartments.
Collectively, our project is highly innovative as it will explore the gut-microbiota crosstalk within the gut in a new dimension by integrating the spatio-temporal host response through combination of up to date genetically engineered mice, gnotobiotic mice, transcriptomics, sequencing technologies and systems biology. Deciphering the complex interactions between the gut microbiota and its host will improve our understanding of human diseases pathogenesis and our discoveries of new therapeutic targets. The intestinal microbiota has been indeed pointed out as a major player in an increasing number of diseases including inflammatory bowel diseases, rheumatoid arthritis, multiple sclerosis, type1 diabetes, obesity or non-alcoholic fatty liver disease.
To achieve our objective, we envisage an integrated "microbiome/immunology" approach by taking advantage of gnotobiotic animals and by using cre-lox and high-throughput sequencing technologies, as well as developing multidimensional statistical models to decipher the dynamic balance established between the commensal microbiota and the host immune system. The four tasks proposed for this project can be done independently but gathering the results will allow us getting a global insight in the physiological role of Card9 and Ripk2 on the Nod2-mediated control of C. rodentium infection. These tasks are respectively:
Task 1: Identify molecular and cellular mechanisms shaping onset of a disease predisposing microbiota.
The respective contributions of Nod2, Ripk2 and Card9 as well as the cellular interaction involved in the genesis of gut microbiota alterations will be determined using not only already generated but also novel genetically engineered mice that are not yet published. This will allow us to identify the common disease-predisposing core within dysbiotic microbiota in the absence of Nod2, Ripk2 or Card9.
Task 2: Identify how disease-predisposing dysbiosis regulates C. rodentium susceptibility.
The intrinsic contribution of Nod2-, Ripk2- and Card9-driven bacterial and fungal dysbiosis on the virulence of C. rodentium will be assessed.
Task 3: Identify gut microbiota-independent role of Nod2, Ripk2 and Card9 on control of Citrobacter rodentium colitis.
The role of Nod2, Ripk2 and Card9 in host defense against C. rodentium will be investigated by using newly-generated germ-free animals.
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Fungal microbiota dysbiosis in IBD
Gut 2016, pii:gutjnl-2015-310746
- Hoffmann TW, Pham HP, Bridonneau C, Aubry C, Lamas B, Martin-Gallausiaux C, Moroldo M, Rainteau D, Lapaque N, Six A, Richard ML, Fargier E, Le Guern ME, Langella P, Sokol H
Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice
ISME J 2016, 10(2):460-77
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Neutralisation of the interleukin-33/ST2 pathway ameliorates experimental colitis through enhancement of mucosal healing in mice.
Gut. 2013 Dec;62(12):1714-23.
- Ubelmann F, Chamaillard M, El-Marjou F, Simon A, Netter J, Vignjevic D, Nichols BL, Quezada-Calvillo R, Grandjean T, Louvard D, Revenu C, Robine S.
Enterocyte loss of polarity and gut wound healing rely upon the F-actin-severing function of villin.
Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):E1380-9.
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NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer.
J Clin Invest. 2013 Feb 1;123(2):700-11.
- Normand S, Delanoye-Crespin A, Bressenot A, Huot L, Grandjean T, Peyrin-Biroulet L, Lemoine Y, Hot D, Chamaillard M.
Nod-like receptor pyrin domain-containing protein 6 (NLRP6) controls epithelial self-renewal and colorectal carcinogenesis upon injury.
Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9601-6.
- Peyrin-Biroulet L, Beisner J, Wang G, Nuding S, Oommen ST, Kelly D, Parmentier-Decrucq E, Dessein R, Merour E, Chavatte P, Grandjean T, Bressenot A, Desreumaux P, Colombel JF, Desvergne B, Stange EF, Wehkamp J, Chamaillard M.
Peroxisome proliferator-activated receptor gamma activation is required for maintenance of innate antimicrobial immunity in the colon.
Proc Natl Acad Sci U S A. 2010 May 11;107(19):8772-7.
- Dessein R, Gironella M, Vignal C, Peyrin-Biroulet L, Sokol H, Secher T, Lacas-Gervais S, Gratadoux JJ, Lafont F, Dagorn JC, Ryffel B, Akira S, Langella P, Nùñez G, Sirard JC, Iovanna J, Simonet M, Chamaillard M.
Toll-like receptor 2 is critical for induction of Reg3 beta expression and intestinal clearance of Yersinia pseudotuberculosis.
Gut. 2009 Jun;58(6):771-6.
- Kobayashi KS, Chamaillard M, Ogura Y, Henegariu O, Inohara N, Nuñez G, Flavell RA.
Nod2-dependent regulation of innate and adaptive immunity in the intestinal tract.
Science. 2005 Feb 4;307(5710):731-4.
- Tanabe T, Chamaillard M, Ogura Y, Zhu L, Qiu S, Masumoto J, Ghosh P, Moran A, Predergast MM, Tromp G, Williams CJ, Inohara N, Núñez G.
Regulatory regions and critical residues of NOD2 involved in muramyl dipeptide recognition.
EMBO J. 2004 Apr 7;23(7):1587-97.
- Chamaillard M, Hashimoto M, Horie Y, Masumoto J, Qiu S, Saab L, Ogura Y, Kawasaki A, Fukase K, Kusumoto S, Valvano MA, Foster SJ, Mak TW, Nuñez G, Inohara N.
An essential role for NOD1 in host recognition of bacterial peptidoglycan containing diaminopimelic acid.
Nat Immunol. 2003 Jul;4(7):702-7.
- Hugot JP, Chamaillard M, Zouali H, Lesage S, Cézard JP, Belaiche J, Almer S, Tysk C, O'Morain CA, Gassull M, Binder V, Finkel Y, Cortot A, Modigliani R, Laurent-Puig P, Gower-Rousseau C, Macry J, Colombel JF, Sahbatou M, Thomas G.
Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease.
Nature. 2001 May 31;411(6837):599-603.