Risk predisposition for Crohn disease A "menage a trois" combining IRGM allele, miRNA and xenophagy

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Autophagy

ISSN: 1554-8627 (Print) 1554-8635 (Online) Journal homepage: https://www.tandfonline.com/loi/kaup20

Risk predisposition for Crohn disease: A “ménage

à trois” combining IRGM allele, miRNA and

xenophagy

Patrick Brest, Pierre Lapaquette, Baharia Mograbi, Arlette

Darfeuille-Michaud & Paul Hofman

To cite this article: Patrick Brest, Pierre Lapaquette, Baharia Mograbi, Arlette Darfeuille-Michaud & Paul Hofman (2011) Risk predisposition for Crohn disease: A “ménage à trois” combining IRGM allele, miRNA and xenophagy, Autophagy, 7:7, 786-787, DOI: 10.4161/auto.7.7.15595

To link to this article: https://doi.org/10.4161/auto.7.7.15595

Published online: 01 Jul 2011.

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Autophagy 7:7, 786-787; July 2011; © 2011 Landes Bioscience

AutophAgic punctum

786 Autophagy Volume 7 issue 7

Punctum to: Brest P, Lapaquette P, Souidi M, Lebrigand K, Cesaro A, Vouret-Craviari V, 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 2011; 43:242–5; PMID: 21278745; DOI: 10.1038/ng.762.

Key words: Crohn disease, inflamma-tory bowel disease, AIEC, microRNA, genome wide association, synonymous polymorphism

Submitted: 03/07/11 Revised: 03/17/11 Accepted: 03/23/11

DOI: 10.4161/auto.7.7.15595

*Correspondence to: Paul Hofman; Email: hofman@unice.fr

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The identification by genome-wide association studies of polymorphisms in autophagy-related genes ATG16L1 (autophagy related 16-like 1) and IRGM (immunity-related GTPase family M) as genetic risk factors for CD onset has further emphasized the involvement of autophagy-related processes in the patho-genesis of inflammatory bowel diseases (IBD). However, it seems puzzling that a general autophagy defect may be asso-ciated with CD. Indeed, autophagy is absolutely required during development and in metabolism since various indi-vidual knockouts of Atg genes are lethal in mice. Moreover, the high prevalence of the CD risk-variants ATG16L1 T300A [minor allele frequency (MAF) 0.49] and

IRGM L105 (MAF 0.1) in unaffected

populations, argues against a general del-eterious autophagy phenotype as being the cause of IBD. As a result, one might

Risk predisposition for Crohn disease

A “ménage à trois” combining IRGM allele, miRNA and xenophagy

Patrick Brest,1,2 _{Pierre Lapaquette,}3,4 _{Baharia Mograbi,}1,2 _{Arlette Darfeuille-Michaud}3,4 _{and Paul Hofman}1,2,5,_*

1_{INSERM ERI-21 and} 2_{Université de Nice Sophia Antipolis; Faculté of Médecine; Nice, France;} 3_{Clermont Université; Université d’Auvergne; Jeune Equipe}

JE2526 and 4_{Institut de Recherche Agronomique (INRA); Unité Sous Contrat USC-2018; Clermont-Ferrand, France;} 5_{Centre Hospitalier Universitaire de Nice;}

Hôpital Pasteur; Human Biobank; Nice, France

expect that disease-associated ATG16L1 and IRGM variants would confer subtle effects on autophagy and disturb one of its functions.

The IRGM region contains mul-tiple polymorphisms that cause tissue-specific variation in IRGM expression. Two polymorphisms of IRGM have been highly associated with CD risk: A “silent” tag-SNP variation within the coding region (c.313C>T); and a 20-kb deletion upstream of the IRGM gene. Of particular interest, the deletion polymorphism is in perfect linkage disequilibrium (r2 _{= 1.0)}

with the tag-SNP; the CD risk haplotype carries both the deletion and the T allele, whereas the protective (reference) haplo-type carries the C allele. It is noteworthy that IRGM expression variations were found to be cell-type dependent. Indeed, HeLa cells heterozygous for IRGM hap-lotypes almost exclusively express the C allele arising from the protective hap-lotype. Similarly, lymphoblastoid cells from heterozygous individuals express the C allele more strongly than the T allele. Conversely, the colon carcinoma cells HCT116 express the CD risk haplotype (T) more strongly than the C allele.

As it has been shown that miRNA can bind to mRNA coding region, we have hypothesized that the synonymous exonic (CTG>TTG, leucine) variant might affect protein expression. Interestingly, we showed both in silico and in vitro that this synonymous variation alters the bind-ing site for the miR-196 family. Ex vivo, miR-196 is overexpressed in the inflam-matory intestinal epithelia of CD patients,

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www.landesbioscience.com Autophagy 787

AutophAgic punctum AutophAgic punctum

due to the overload of available lysosomal compartments. Given that the miR-196 family is overexpressed in the inflamma-tory intestinal epithelia, these observa-tions might highlight the importance of such a tissue-specific expression in CD. We therefore propose a model in which a “ménage à trois” combining expression levels of IRGM allele, miRNA expression and bacterial load are all critical for indi-vidual risk predisposition for CD.

In conclusion, autophagy is upregu-lated to cope with environment stress. It is well established that transcription of several genes (BECLIN 1, ATG1, ATG4,

ATG7, ATG8 and IRGM) helps to

fine-tune the autophagy process. Another level of control that emerges is the effect of miRNAs (miR-30A and miR-196) on autophagy. One should consider that reg-ulation of autophagy by transcription is often a slower “on-off switch” process (cis effect), whereas miRNA are “ideal ther-mostats” that buffer it (trans effect). Such complex genetic and epigenetic regula-tions are essential since downregulation of autophagy is involved in a growing list of pathologies including neurodegenerative diseases, cancer, and herein inflamma-tory diseases. The unexpected miRNA-based alteration in allele expression, we evidenced, represents not only a new pathological paradigm but also opens new avenues for theragnostic purposes. the pathogen-containing phagosome as

it matures. Similarly, we have shown that expression of human IRGM confers pro-tection against infection of CD-associated Adherent-Invasive E. coli (AIEC). It has been proposed that IRGM may protect the host against intracellular bacteria by, (a) driving vesiculation and disruption of the phagosome leading to the release of the pathogen out of its protective niche into the cytosol; (b) driving the engulfment of bacteria into large autophagic vesicles through addition of IRGM-containing vesicles; and, (c) by targeting the patho-gen for lysosomal degradation using an autophagy-dependent mechanism.

Our observation, in agreement with previous data from other groups, con-firmed that overexpression of IRGM protein in epithelial cells leads to an accu-mulation of autophagosomes containing bacteria due to the decrease in lysosomal fusion. Importantly, we showed that miR-196 overexpression, as does siRNA, is able to decrease IRGM level and thereby autophagy initiation. Hence, we demon-strated that IRGM level is tightly regu-lated by miR-196. We proposed that in IRGMC_{-expressing cells, the xenophagy}

flux is well-regulated leading to bacteria clearance (Fig. 1). By contrast, in IRGMT

-expressing cells, the absence of IRGM regulation by miRNA may lead to an accumulation of intracellular pathogens where it downregulates the IRGM

pro-tective variant (c.313C) but not the risk-associated allele (c.313T). Moreover, we showed that this nucleotidic sequence of regulation is extremely conserved through mammal evolution, suggesting the impor-tance of this gene in the efficiency of the autophagic response.

Of particular interest, we provide evi-dence that such a miR-196/allele couple modulates the function of IRGM in autophagy. The human IRGM is cur-rently a poorly understood regulator of xenophagy, a dedicated form of autophagy that engulfs and degrades intracellular pathogens as a host-defense mechanism. The human IRGM belongs to the p47 Immunity-Related GTPase (IRG) fam-ily, which is strongly involved in innate resistance mechanisms against intra-cellular pathogens (Gram-positive and Gram-negative bacteria, mycobacteria and protozoans). However, the human IRGM has a truncated GTP-binding domain and its GTP-binding properties have not yet been explored. In uninfected epithelial cells, the IRG proteins reside in the endo-plasmic reticulum and the cis-Golgi com-plex. Upon infection, the murine Irgm1 proteins translocate within minutes to the plasma membrane at the phagocytic cup as a pathogen (e.g., Mycobacterium

tuberculosis; Listeria monocytogenes) enter

into the cell, and remain associated with

Figure 1. proposed regulation of miRnA regulation of iRgm haplotype on xenophagy. Autophagy is a vesicular pathway, enabling cells to digest their

own cytosol or invasive bacteria. During autophagy, a portion of cytosol is sequestered within a double-membrane vesicle, called an autophagosome. the autophagosome is formed by expansion of a phagophore, the origin of which remains unknown. During the maturation step, the autophago-some acquires an acidic ph and hydrolases by fusing with a lysoautophago-some to generate an autolysoautophago-some in which the content is degraded. it is proposed that iRgm may protect the host cells against bacteria by (A) driving vesiculation and disruption of the phagosome, releasing the pathogen out of its protective niche into the cytosol (inset), (B) directing the engulfment of bacteria by large double-membrane autophagosomes and (c) targeting the pathogen for lysosomal degradation by promoting autolysomal maturation. however, this process may be altered in diseases such as crohn disease.